First Gen:
Bulbasaur/Ivysaur/Venusaur: Toads with dinosaur-like characteristics. Note: they have sprawled legs, which are not what dinosaurs had. Toads do not hop all the time, they sometimes crawl.
Charmander/Charmeleon/Charizard: Charmander is a salamander, which in folklore is associated with fire, Charmeleon is a hadrosaur/salamander mix, and Charizard is your typical western dragon
Squirtle/Wartortle/Blastoise: Squirtle and Wartortle look tons like the Seychelle terrapin (and Squirtle's Japanese name is the same as the zenigame), Wartortle is a minogame, while Blastoise is a tortoise/tank mix (note the large canons on its back :P)
Caterpie/Metapod/Butterfree: Caterpie is a spicebush swallowtail butterfly caterpillar (1 2) with its osmeterium (the pink forked thing) permanently extended, while Metapod is a Pieris Rapae pupa (link) and Butterfree may be a black-veined white butterfly
Weedle/Kakuna/Beedrill: Stages of bees, and wasps. Bee larva (this, the originally linked picture, is a bee moth larva, hence the "AphoSoc" at the end of the url is short for Aphomia sociella), bee pupa, and a wasp
Pidgey/Pidgeotto/Pidgeot: Pidgey looks far more like a cedar waxwing or a female northern cardinal than any pigeon I've ever seen, while Pidgeotto and Pidgeot are more like hawks or falcons
Rattata/Raticate: Rat and nutria ( 1 2). ratatosk
Spearow/Fearow: Some sort of hawk and crane/condor. Octoboy suggests that fearow is a chimera of a bunch of different birds. Anyone have a specific species?
Ekans/Arbok: Generic snake and cobra - both represent a venomous snake as well as a constrictor.
Pikachu/Raichu: Mountain viscacha and kangaroo rat? Though similarly named, it is suggested that Pikachu is NOT based on the pika.
Sandshrew/Sandslash: Pangolin and porcupine/giant armadillo
Nidoran-F/Nidorina/Nidoqueen: Rabbits and, with 'Rina, rhino (which you can especially see in Nidorina's joints) baragon
Nidoran-M/Nidorino/Nidoking: Rabbits and, with 'Rino, rhino (which you can especially see in Nidorino's joints) baragon
Clefairy/Clefable: Fairies
Vulpix/Ninetales: Red fox/kitsune and kyuubi kitsune (nine-tailed kitsune)
Jigglypuff/Wigglytuff: Balloons with cat/rabbit ears
Zubat/Golbat: Generic bats
Oddish/Gloom/Vileplume: Leshy, mandrake, rafflesia
Paras/Parasect: Cicada nymph and hermit crab (1 2) Kingler's Kindom does an in-depth profile of a paracitic fungus, a cicada nymph, and the red, spotted mushroom on its back.
Venonat/Venomoth: Moth flies?
Diglett/Dugtrio: Bop-a-moles, Dosojin
Meowth/Persian: Maneki neko/seal point ragdoll cat, persian cat, and cougar
Psyduck/Golduck: Platypus and kappa
Mankey/Primeape: Pygmy marmoset
Growlithe/Arcanine: Shishi
Poliwag/Poliwhirl/Poliwrath: Tadpoles
Abra/Kadabra/Alakazam: ? (Abra looks slightly like a possom to me, and stromdusk suggests coyote). Abra is based on Edgar Cayce, the "Sleeping Prophet"; Kadabra is based on Uri Geller, the Israeli spoonbender; Alakazam's Japanese name is based on Houdini, but it the creature appears to be merely an exaggeration of Kadabra.
Machop/Machoke/Machamp: American wrestlers/Dilophosaurs - could also share the same origin as Goro (see Ledian, Metang, and Salamence)
Bellsprout/Weepinbell/Victreebel: Pitcher plants
Tentacool/Tentacruel: Jellyfish
Geodude/Graveler/Golem: Rocks and boulders and stones oh my!
Ponyta/Rapidash: Generic horse and unicorn... ON FIRE!
Slowpoke/Slowbro: Perhaps pygmy hippos!
Magnemite/Magneton: Magnets
Farfetch'd: Duck with leeks dish; also maybe samurai
Doduo/Dodrio: Kiwis/rheas
Seel/Dewgong: Harp seal and dugong/manatee/monk seal
Grimer/Muk: Sludge
Shellder/Cloyster: Scallop and oyster
Gastly/Haunter/Gengar: Hitodama/Sogen-bi; partially formed ghost; doppelgänger
Onix: Wyrm? (HT thinks earth dragon)
Drowzee/Hypno: Tapir baku and hypnotist
Krabby/Kingler: Generic crab and fiddler crab
Voltorb/Electrode: Pokéball mimics or ball lightning
Exeggcute/Exeggutor: Eggs and coconut tree
Cubone/Marowak: One idea is that they're prarie dogs wearing those cow skulls you find in the desert. Others say they're too reptilian, and think they might be based on a Pachycephalosaurus skull. The Pachycephalosaurus was a dinosaur whose skull was very thick at the top.
Hitmonlee: kickboxer Sawamura Tadashi, looks like a blemyae also
Hitmonchan: boxer Ebihara Hiroyuki
NOTE: Hitmonlee and Hitmonchan are NOT based on Jackie Chan OR Bruce Lee. Anyone who says that again, I will report their post as spam. Have a nice day
Lickitung: ? (absol attacker suggested that there may be some albino fat-tailed gecko [1 2])
Koffing/Weezing: Air pollution/sea mines
Rhyhorn/Rhydon: Rhinos
Chansey: Good mother/nurses and luck. I believe it is based on the Chinese custom to paint eggs red for good luck, as it is a pink, egg shaped pokemon, which is said to be good luck. - Octoboy (source?)
Tangela: Mess of vinelike seaweed
Kangaskhan: Kangaroo or Procoptodon
Horsea/Seadra: Sea horses. It's spitting ink ability is like that of an archer fish.
Goldeen/Seaking: Tosakin goldfish and calico ryukin goldfish, and the horn possibly came from Matsya, an avatar of Vishnu
Staryu, Starmie: Starfish and sunstar
Mr. Mime: Mime
Scyther: Mantis.
Jynx: Yuki-Onna/? (There was an argument on the old thread on whether or not she was based on ganguro or Yamanba. It starts here, goes on to page 9, skips a few pages, then there's a rebuttal here on page 13.)
Electabuzz: Oni
Magmar: Fire breather? Karura
Pinsir: Male stag beetle
Tauros: Bison
Magikarp/Gyarados: Chinese legend of a carp turning into a sea serpent/dragon
Lapras: Plesiosaurus/sea turtle
Ditto: Silly putty, clay, and, as Yami_no_Waru puts it, "the same Japanese myth Kirby and Buu (Dragonball) do, about a pink demon that could consume enemies and mimic their abilities"
Eevee: Fennec fox and/or maybe Blanford's fox, houkou in theory. A fox-like youkai with several elemental powers.
Vaporeon/Jolteon/Flareon: Foxes? with cat/dog characteristics: mermaid, electric dog-thing, and fire... foxy?-thing, respectively.
Porygon: Polygons/? (HT said parrot/duck)
Omanyte/Omastar: Ammonites
Kabuto: Horseshoe crab [Japanese name for Horseshoe crab is Kabutogani], trilobite
Kabutops: Trilobite skeleton/mantis
Aerodactyl: Long-tailed pterosaur
Snorlax: Gluttony/bear/Totoro?
Articuno: Quetzal, Bird-of-Paradise
Zapdos: Native American Thunderbird; its long thin beak is reminiscent of a hummingbird (or something)
Moltres: Arabian/Western/Russian phoenix
Dratini/Dragonair/Dragonite: Water dragons (I seriously doubt that Barney was an inspiration for Dragonite)
Mewtwo: Cat-human, some think that it's a more developed embryo (see below)
Mew: Kitten/gerbil/embryo
Second Gen:
Chikorita/Bayleef/Meganium: Sauropods
Cyndaquil/Quilava/Typhlosion: Cyndaquil is an echidna, while Quilava is a weasel and Typhlosion is a honey badger (1 2)
Totodile/Croconaw/Feraligatr: Alligators (1 2).
Sentret/Furret: Flying Squirrel. Furret, as its name implies, is a ferret
Hoothoot/Noctowl: Owls. Hoothoot looks like a Pygmy owl; Noctowl looks like an Eagle owl.
Ledyba/Ledian: Ladybird Beetles, of course. Ledian may also have some basis in Pulseman (1 2).
There could also be some Ganbaron in there, too.
Spinarak/Ariados: Happy face spider and some other spider
Crobat: Vampire bat
Chinchou/Lanturn: Angler fish
Pichu: Generic mouse?
Cleffa: Fairy
Igglybuff: Balloon
Togepi/Togetic: Togepi is an egg, Togetic is a fairy
Natu/Xatu: Based off of Native American totem poles. (Xatu resembles the Thunderbird)
Mareep/Flaaffy/Ampharos: Sheep; partially shaved sheep; totally shaved sheep(?)/lighthouse
Bellossom: "Grass-skirt girl" hula (1 2) dancer
Marill/Azumarill: Marill is a ? (WG said pika), Azumarill is a rabbit
Sudowoodo: Petrified tree
Politoed: Toad
Hoppip/Skiploom/Jumpluff: Stylized dandelions
Aipom: A monkey (perhaps a spider monkey) with an exaggeration of the monkey's prehensile tail. A link to Ahuizotl (Aztec god that's a cross between a dog and a monkey, with a hand on the end of its tail) was also suggested.
Sunkern/Sunflora: A seed and a sunflower
Yanma: Red dragonfly
Wooper/Quagsire: Axolotl and giant salamander
Espeon: Nekomata
Umbreon: Witch's cat
Murkrow: Crow with a witch hat and broom tail
Slowking: Hippopotamus?
Misdreavus: Banshee / Nukekubi
Unown: Living alphabet letters
Wobbuffet: Full-sized punching bag? and Sanpei Hayashiya
Girafarig: Giraffe - The Japanese name (Kirinriki) is a palindrome, meaning it can be read the same forward and back. The Japanese word for 'giraffe' is Kirin (the same as the legendary creature). The dual normal/psychic type covers the most popular weakness of each type. Psychic prevents normal's fighting weakness and normal prevents psychic's ghost weakness. Bug and Dark type attacks still affect Girafarig; though with the 2nd generation, dark types were relatively rare.
Also: "The pushmi-pullyu (pronounced like "push-me-pull-you") is a fictional breed of antelope in the Doctor Dolittle novels and the 1967 film. The pushmi-pullyu is a two headed antelope; the two heads are at opposite ends of the body. Both heads act as though they are on the front of the body, and when prompted to move, both attempt to move forwards. Unsurprisingly, this makes guiding the pushmi-pullyu a difficult task." (noted by Octoboy, supplimented by Kthleen)
Pineco: Bagworm/pinecone
Foretress: Bagworm/(either a turret, giant clam, or both)
Dunsparce: Tsuchinoko, aka bachi-hebi (1 2 3)
Gligar: Scorpion/gargoyle
Steelix: Wyrm?
Snubbull/Granbull: Bulldogs
Quilfish: Blowfish
Scizor: Mantid
Shuckle: Scale insect (maybe Ceroplastes rusci ]), and perhaps the worm in the apple
Heracross: Japanese rhinoceros beetle
Sneasel: Kamaitachi
Teddiursa/Ursaring: Teddiursa is a teddy bear/bear cub, Ursaring is a sun bear
Slugma/Magcargo: Slugma is a slug, Magcargo is a snail
Swinub/Piloswine: Inobuta boar-pig and some sort of boar/mammoth mix
Corsola: A chunk of coral
Remoraid/Octillery: Remoraid is an archer fish/remora (1 2 3) and a gun, perhaps a pistol; Octillery is an octopus
Delibird: Rockhopper penguin/Santa.
Mantine: Manta ray
Skarmory: Stymphalian birds/Andean condor with a Marabou stork beak, armored crane
Houndour/Houndoom: Doberman Pinschers/hell-hounds (like cerberus, only one head)
Kingdra: Weedy sea dragon and/or Leafy sea dragon
Phanpy/Donphan: Very short elephant and elephant/tire
Porygon2: Toy drinking bird
Stantler: Caribou
Smeargle: Beagle?/lemur? (read the second paragraph under ‘Behavior’) / artist
Tyrogue/Hitmontop: Are humans that embody different fighting styles (Hitmontop = Capoeira)
Smoochum: Baby Jynx
Elekid: Plug
Magby: Perhaps another mythical salamander
Miltank: Cow
Blissey: Good mother/nurses and luck
Raikou: Smilodon, raiju
Entei: Fuu dog/Shishi
Suicune: The connection with the North and its dog-like shape lead some to believe that it is based on a wolf; the facts that the other two are based on cats and that it has a comparatively short and wide muzzle lead some to believe that it is based on the cheetah; the facts that it is known to purify water and that it has this large thing sticking out of its head lead some to believe that it is also partially based on the unicorn/kirin. Heck, it's probably a mix.
Komedic Konservationist has suggested the civet (Civet standing and Suicune in a somewhat similar pose), but then revised it to a
Larvitar/Pupitar/Tyranitar: dinosaurs of some sort? Perhaps monitor lizards
Lugia: Gray heron (there's one that looks like Lugia on the cover of Across the Nightingale Floor)/dragon partner to the phoenix/Halcyon, also Susa-no-o
Ho-oh: Ho-Oh, the Japanese phoenix/phoenix partner to the dragon, also Amaterasu
Celebi: A chibi forest fairy
Third Gen:
Treecko: Leaf-tailed gecko
Grovyle: Leaf-tailed gecko , and deinonychosaur has been suggested due to its shape and it having feathers
Sceptile: Green basilisk /Leaf-tailed gecko (Pokémon of the Day Chick thinks that Sceptile's tail looks like part of a juniper bush. I do, too. X) ) Also, Porygandrew thinks that the yellow "seeds" on its back has to do with cupping. Perhaps someone can find a plant that looks like Sceppy's tail and has large yellow seeds?
Torchic/Combusken/Blaziken: Chick and cockfighting chickens/harpy (Blaziken has some basis in the bantam rooster, and absol attacker suggested garuda ), resembles Horus or Ra
Mudkip/Marshtomp/Swampert: Mudskippers /blue axolotls , and Swampert may have some bunyip in it
Poochyena/Mightyena: Brown hyenas (Cub) Beast of Gévaudan (thanks to GentleArtillery)
Zigzagoon: Raccoon dog (aka tanuki)
Linoone: Zorilla
Wurmple, Silcoon/Cascoon: Stinging rose caterpillar ? and luna moth pupae in the early stages
Beautifly: Old world swallowtail butterfly
Dustox: Female luna moth with some male gypsy moth mixed in
Lotad: Lilypad/chibi kappa ; may be a pun on "duckweed" (look at this anyway!)
Lombre: Lilypad/sombrero/stereotypical Mexican/kappa
Ludicolo: Dancing sombrero, pineapple, Mariachi, kappa-type thing
Seedot: Acorn
Nuzleaf/Shiftry: Konoha tengu
Taillow: Welcome swallow
Swellow: Barn swallow
Wingull: Gull, likely ring-billed
Pelipper: Pelican
Ralts/Kirlia/Gardevoir: A tomboy, a ballerina, and a fairy tale princess/adult graceful woman dancer
Surskit: Pondskater /harvestman
Masquerain: Lanternfly with eye mimicry
Shroomish: Mushroom
Breloom: Othnelia /kangaroo?/mushroom
Slakoth: Sloth
Vigoroth: Sloth, Megalonychid ground sloth (info on Megalonychids and Megatherium )
Slaking: Megatherium/gorilla
Nincada: Cicada nymph (the Pokémon Zoology page points out that Paras more correctly represents one)
Ninjask: Adult cicada
Shedinja: A shed cicada exoskeleton
Whismur: Jar/rabbit? Family is based on sound getting progressively louder
Loudred: Boombox (it has woofers for ears).... absol attacker thinks that there's some Taz in it :P
Exploud: Pipe organ, also some howler monkey
Makuhita/Hariyama: Sumo wrestlers
Azurill: Unevolved Marill->mouse? (They were just working backwards.)
Nosepass: Moai/compass
Skitty and Delcatty: Cats
Sableye: Troll/goblin
Mawile: Bear trap, Futakuchi-onna(why didn't I see this one before >.<)
Aron: Funky protoceratops-type thing
Lairon: Bigger funky ceratopsian
Aggron: Diceratops
Meditite/Medicham: Yogis
Electrike: ? (stromdusk suggested Parson Jack Russell terrier)
Manectric: German shepherd? (and quilava plush suggested maned wolf, but I have a stronger feeling toward the G.S.). If anything, it's at least canine-based. Also based on the raiju
Plusle: Rodent/lagomorph+positive charge
Minun: Rodent/lagomorph+negative charge
Volbeat/Illumise: Firefly
Roselia: Woodland sprite/roses
Gulpin/Swalot: Stomachs, blob fish (sidenote: blob fish are part of a family of bottom-dwelling fish called 'sculpins')
Carvanha: Red-bellied piranha
Sharpedo: Great white shark/ocean sunfish/Mola Mola. It's name (samehada) comes from a legend based on the Isonade - "Samehada" is Isonade's Subordinate. 'Samehada' means Shark-Skin.
Wailmer: Blue whale/ball
Wailord: Blue whale/basilosaurus
Numel: Dromedary (Arabian) camel (the two major types of camel ) / Tyrannotaur states that the volcano is specifically a dome volcano . The green part resembles moss or foliage growing on the volcano.
Camerupt: Bactrian camel/shield volcano
Torkoal: Red-foot tortoise /coal - Also the Kotasu
Spoink/Grumpig: Pigs (maybe somebody saw this website ! XD), perhaps the biblical "neither cast ye your pearls before swine" (Matthew 7:6) was snuck in there as well
Spinda: A drunk, tiny, pinkish and tan panda?/teddy bear brought to life? Could have gotten its red color from the Red Panda or it could be part of getting a red face from drinking a lot, a concept (being drunk) that's part of Drunken Boxing. Why a panda? Who knows...
Trapinch: Antlion larva
Vibrava: Adult antlion /faerie dragon
Flygon: Green lacewing /faerie dragon
Cacnea: Barrel cactus
Cacturne: Saguaro cactus/scarecrow
Swablu: White-winged fairy-wren (1 2 )/cotton
Altaria: Golden fleece-guarding dragon?/white-winged fairy-wren/cotton/cloud
Zangoose: A mongoose/cat. The rivalry with Seviper is based on how mongooses can sometimes eat snakes. (Remember The Ghost of Maiden's Peak ?)
Seviper: Seviper: A viper called habu
Lunatone: Moon
Solrock: Sun
Barboach: Loach/(mudfish /mud-minnow )
Whiscash: Legend of a giant catfish who causes earthquakes (and maybe the wels cat [1 2 ])
Corphish/Crawdaunt: Crayfish
Baltoy: Shakou /spinning top
Claydol: Shakou
Lileep/Cradily: Coral polyps (1 2 )/crinoids (sea lilies), or tunicate.
Anorith/Armaldo: Anomalocaris
Feebas: An odd bass? It looks a lot like this red-bellied piranha to me....
Milotic: Sea serpent/siren with greatly enlongated gills (if you want to Google image search a siren, search "sirenidae"), and it could perhaps be Magikarp/Gyarados' opposite
Castform: Cloud, weather conditions
Kecleon: Chameleon, Crested Gecko [1]
Shuppet: A haunted tissue ghost
Banette: A haunted marionette and voodoo doll.
Duskull: Grim reaper sans scythe/Hitotsume-Kozou/Dokuro
Dusclops: Mummy-wrapped cyclops-ghoul
Tropius: Apatosaurus /banana tree
Chimecho: One of those wind chimes that look like an upside-down cup with a tassel/paper hanging out of it (something like this , but different)
Absol: Barghest , perhaps with some mountain goat
Wynaut: Small punching bag? It's in the sillohuette of a person shrugging. Also based on a Japanese comedian?
Snorunt: A person wearing a straw blanket thing (pic from Zeta), or perhaps ]ame-furi-koz?
Glalie: Getter Robo head/hail
Spheal: Spotted seal with ears/ball (sea lions have external ear projections and real seals don't)
Sealeo: Harbor seal
Walrein: Walrus
Clamperl: Giant clam
Huntail: Gulper Eel (1 2 )/Viperfish
Gorebyss: Oarfish /pipefish, or chimera (thanks to Absol Attacker)
Relicanth: Coelacanth
Luvdisc: Discus fish / kissing gourami / "heart" shape
Bagon: Baby western dragon and perhaps Pachycephalosaurus
Shelgon: Dragon cocoon?
Salamence: Adult western dragon/Devilman
Beldum/Metang/Metagross: Sci-fi invader robots? Beldum, at least according to its name, may be based on a dumbbell; ?Ins0mnIac? has pointed out that Metang looks like this thing from Gundam (what's it called?) and Metagross looks like a Tektite from one of the Zelda games
Regirock/Regice/Registeel: Jewish golems with braille eyes
Latias/Latios: Dragons/jet planes? Stylized griffins?
Kyogre/Groudon: An orca and an upright armadillo lizard (1 2 ) cast in roles vaguely similar to the Biblical Leviathan and Behemoth, respectively
Rayquaza: Eastern dragon (that looks somewhat like a lindworm) cast in a role vaguely similar to the Ziz , to complete the Behemoth/Leviathan/Ziz motif
Jirachi: Tanabata festival/genie (Jirachi has three green tanzaku on it)
Deoxys: Humanoid alien/mutated virus-DNA.... Kthleen's brother thinks it looks like an orbital frame from Zone of the Enders. Red Baron, 2
Fourth Gen:
Turtwig, Growtle, Torterra: snapping turtle, Anklyosaur or Nodosaur [1], as well as the hindu Akupara
Chimchar, Monferno, Infernape: stylized chimpanzee, Sun Wukong, circus monkeys
Puplip, Prinplup, Empoleon: Magellanic penguin, Emperor Penguin/ King Penguin
Starly, Staravia, Staraptor: gray starling, Gambel's Quail?
Bidoof, Bibarel: Beaver/marmot-type animal.
Kricketot: Black Spotted Leaf Beetlekuroboshi tsutsuhamushi
Kricketune: cricket/Guitar Beetle - supplimented by its pokedex entry mentioning music, a feature grasshoppers/crickets' chirps are known for. It is shaped like a double bass.
Shinx, Luxio, Luxray: Kimba! I mean... feline/ lion. Komedic Konservationist says it could also be based off of the star constellation Leo
budew: Probably a rose bud (see roselia)
Roserade: a boquet (see roselia)
Cranidos, Rampardos: a type of Pachycephalosaur
Sheildon, Bastiodon: Ceratops
Burmy, Wormadam, Mothim: Caddis Worm, Bagworm.
combee, Vespiquen: honeybees/Hive, queen bee as well as some wasp [1,2]
Pachirisu: Squirrel
Buizel, Floatsel: Otter? Weasel? Both? Something like that.
Cherubi, Cherrim: Cherry Blossom seed & flower
Shellos, Gastrodon: sea slug - Nudibranchs, thanks to Ophie
Ambipom: (see aipom)
Drifloon, Drifblim: balloons (and weights) / weather or hot-air balloons
Buneary, Lopunny: rabbits
Mismagius: witch-like (see misdreavus)
Donkrow: mobster/gangster - read pokedex entry (see murkrow)
Glameow, Purugly: cats
Chingling: bell (see chimecho)
Stunky, Skuntank: skunks and the su
Bronzor, Bronzong: Dotaku as well as the tale of the mirror and the bell (explains the resisting heat thing, too).
Bonsly: Bonsai/petrified tree
Mime Jr.: Clown/mime/mane (a sort of clown or comic who imitates people for amusement)
Happiny: An egg. According to Absol Attacker & Kthleen, it also stems from the concept of schoolkids learning parenting skills by carrying around an egg [1](see Chansey/Blissey)
Perap: Masked lovebird (a type of parrot) with a music note head
Spiritomb:Spiritomb appears to be some kind of spirit coming out of something on the ground. So, I think it might be based off of a djinn, or some kind of evil jar-dwelling monster that appears in a number of RPGs.(Yamato-San) - May also be based on the Orochi legend.
Gible, Gabite, Garchomp: Landsharks, hammerhead shark, jet
Munchlax: Totoro? (See Snorlax)
Riolu, Lucario: Anubis/jackal, coyote, canine/ninja
Hippopotas, Hippowdon: Hippos (moreso than slowpoke)
Scorupi, Drapion: Emperor Scorpion
Croagunk, Toxicroak: fighting frogs / Poison Dart Frogs
Carnivine: Venus-Flytrap plus...something that gives it levitate. o_O;;
Finneon, Lumineon: butterfly-tail goldfish
Mantyke: Manta ray (baby Mantine)
Snover, Abomasnow: based off of the Yukionna ala Jynx? Could also be a Yeti+Conifer or a daikon radish
Weavile: Kamaitachi (see Sneasel)
Magnezone: UFO? 'coil' more than likely comes from a tesla coil (see Magneton)
Lickylicky: (see Lickitung)
Rhyperior: (see Rhydon)
Tangrowth: (see Tangela)
Elecable: (reminds me of This Guy (see Electabuzz)
Magmortar: (see Magmar)
Togekiss: Dove (see Togetic)
Megayanma: prehistoric dragonfly, Meganeura (see Yanma)
Leafeon: (see Eevee)
Glaceon: (see Eevee)
Gliscor:: chupacabra? vampire bat (see Gligar)
Mamoswine: partly-mammoth, partly pig/boar/razorback (see Piloswine)
PorygonZ: Hummingbird design (see Porygon 2) The pokedex entry says: "Although program was added in order to make it surpass other pokemon, it began to have strange behaviours." which could represent evolving A.I. or as Yami ookami pointed out, a glitch in the programming. the 'Z' represents the Z axis in space (XYZ).
Gallade: could be based off of Maculele, a brazilian dance with sticks.
Probopass: Mr. Potato(moto) Head or Groucho Glasses(see Nosepass). Still could be based off of Easter Island heads (see Nosepass)
Dusknoir: genie (see Dusclops)
Frosslass:Yuki-On-Na (see snorunt)
Rotom: electrical discharge / Plasma / Pulseman
Azelf, Uxie, Mesprit: Yukishii (knowledge pokemon) could represent a brain,
Dialga: Absol Attacker says it could be a 'Cyborg Dinosaur' melding past and future together.
Palkia: Absol Attacker says the things on its arms could resemble satelite dishes. I see an old-fashioned godzilla-esque monster thrown in there for good measure.
Manaphy: Possibly a sea angel, sea butterfly, or Cliolima,
Heatran: volcano embodiment?
Regigigas: (see the Regis)
Giratina: Bobbit Worm. Centipede/Basilisk and 'guillotine' part (though technically that should be in name-origins thread. Guardian of the Void sounds good as a third counterpart to Dialga/Palkia.)
Cresselia: a swan, probably based on Cygnus, the swan constellation as well as the crescent moon.
Fione: poor-man's Manaphy (the 'tiny-tim' if you will)
Darkrai: Ghost? embodied Nightmare?
Shaymin: Chia pet.... Or Echidna.
Aruseus: Arseus seems to be a cross between an elegant, four-legged mammal and a horse. It may be based on a centaur. Its body is white and Arseus has a gold wheel around its abdomen. It has gold hooves attached to its four legs. Its hair is quite long and its face is green. It may be a reference to the Chinese mythical creature, the qilin (??). It also bears resemblance to the forest spirit Shishigami in the Hayao Miyazaki film Princess Mononoke.
Arseus is classified as the "Creation Pokémon". Legend says this Pokémon used 1,000 of its arms to create the universe. Its name is partially derived from Zeus, the ruler of Mount Olympus in Greek Mythology. Also, Zeus was called Jupiter by ancient Romans. In astrology, the planet Jupiter rules the sign Sagittarius, which has a centaur as a symbol. This may be why Arseus resembles a horse.
Nidoking/queen, Tyranitar, and Agrron all have roots in Godzilla like monsters. Aggron seems to have more relation to some of the newer Ultraman Monsters though.