*steals from Serebii forums and tweaks* <_< >_>
HoundoomTrainer gathered the 1st gen, Wolf Goddess gathered 2nd gen, I'm gathering 3rd (pg. 6 on the Serebii link) and maybe 4th 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 mythology is associated with fire, Charmeleon is a hadrosaur/salamander mix, and Charizard is your typical western dragon
Squirtle, Wartortle, Blastoise: Squirtle and Wartortle are river turtles, 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 pupa (anyone know what species this is?) 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 is a cedar waxwing, while Pidgeotto and Pidgeot are more like hawks or falcons
Rattata, Raticate: Rat and nutria
Spearow, Fearow: Some sort of hawk and crane/condor
Ekans, Arbok: Generic snake and cobra
Pikachu, Raichu: Generic rodent and kangaroo rat?
Sandshrew, Sandslash: Pangolin and porcupine/giant armadillo
Nidoran-F, Nidorina, Nidoqueen: Rabbits
Nidoran-M, Nidorino, Nidoking: Rabbits
Clefairy, Clefable: Fairies?
Vulpix, Ninetales: Kitsune and kyuubi kitsune (nine-tailed kitsune)
Jigglypuff, Wigglytuff: Balloons?
Zubat, Golbat: Generic bats
Oddish, Gloom, Vileplume: Radish, rafflesia
Paras, Parasect: Cicada nymphs
Venonat, Venomoth: ? and a moth
Diglett, Dugtrio: Bop-a-moles XD
Meowth, Persian: Maneki neko and cougar
Psyduck, Golduck: Platypus and kappa
Mankey, Primeape: Generic monkeys/apes
Growlithe, Arcanine: Fuu dog
Poliwag, Poliwhirl, Poliwrath: Tadpoles
Abra, Kadabra, Alakazam: ? (Abra looks slightly like a possom) (stromdusk suggests coyote)
Machop, Machoke, Machamp: American wrestlers/Dilophosaurs
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: 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, 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
Exeggcute, Exeggutor: Eggs and coconut tree
Cubone, Marowak: ? (HT thinks possible prarie dogs)
Hitmonlee: kickboxer Sawamura Tadashi
Hitmonchan: boxer Ebihara Hiroyuki
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
Tangela: It's a bush. X)
Kangaskhan: Kangaroo or Procoptodon
Horsea, Seadra: Sea horses
Goldeen, Seaking: Ryukin goldfish (red-and-white and calico, respectively)
Staryu, Starmie: Sunstars (1 2)
Mr. Mime: Mime
Magmar: Fire breather?
Pinsir: Male stag beetle
Magikarp, Gyarados: Japanese legend of a fish turning into a sea serpent
Lapras: Plesiosaurus/sea turtle
Ditto: Silly putty? 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, Vaporeon, Jolteon, Flareon: Fennec foxes with cat/dog characteristics
Porygon: ? (HT said parrot/duck)
Omanyte, Omastar: Ammonites
Kabuto, Kabutops: Kabuto (samurai helm), trilobite/mantis
Articuno: Quetzal and Arabian anka
Zapdos: Ok some sort of electricity-bird
Moltres: Arabian/Western/Russian phoenix
Dratini, Dragonair, Dragonite: Water dragons (I severly doubt that Barney was an inspiration for Dragonite)
Mewtwo: Cat-human, some think that it's a more developed embryo (see below)
Mew: Kitten, some see a connection with embryos
Cyndaquil/Quilava/Typhlosion: Cyndaquil is an echidna, while Quilava is a weasel and Typhlosion is a European badger.
Sentret/Furret: Sentret seems to be a mix of squirrel with rabbit. 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 seems to have a bit of alien mixed into it.
Spinarak/Ariados: Happy face spider and some other spider
Crobat: Vampire bat
Chinchou/Lanturn: Angler fish
Pichu: Generic mouse?
Togepi/Togetic: Togepi is an egg, Togetic is a fairy
Natu/Xatu: Based off Native American totem poles. (Xatu resembles the Thunderbird)
Bellossom: Some sort of flower
Marill/Azumaril: Marill is a ? (WG said pika), Azumarill is a rabbit
Sudowoodo: Petrified tree
Hopip/Skiploom/Jumpluff: Mountain groundsel (1 2)?
Aipom: Generic monkey with emphasis om the prehensileness of the tail
Sunkern/Sunflora: A seed and a sunflower
Yanma: Red dragonfly
Wooper/Quagsire: Axolotl and giant salamander
Espeon/Umbreon: Espeon is a Nekomata, while Umbreon is a fennec fox
Murkrow: Crow with a witch hat and broom tail
Unown: Living hieroglyphics
Wobbuffet: Full-sized punching bag and Sanpei Hayashiya
Foretress: Bagworm/(either a turret, giant clam, or both)
Dunsparce: Some kind a larva/pupa?
Schuckle: Scale insect
Heracross: Rhinoceros beetle
Teddiursa/Ursaring: Teddiursa is a teddy bear/bear cub, Ursaring is a sun bear (1 2)
Slugma/Magcargo: Slugma is a slug, Magcargo is a snail
Swinub/Piloswine: Inobuta boar-pig and some sort of boar
Corsola: A chunk of coral
Remoraid/Octillery: Remoraid is an archer fish/remora (1 2 3); Octillery is an octopus
Delibird: Rockhopper penguin/Santa.
Mantine: Manta ray
Skarmory: Stymphalian birds/Andean condor with a Marabou stork beak
Houndour/Houndoom: Doberman Pinschers/hellhounds (WG said "Cerebus")
Kingdra: Weedy sea dragon
Phanpy/Donphan: Very short elephant and elephant/tire
Porygon2: Toy drinking bird
Tyrogue/Hitmontop: Are humans that embody different fighting styles (Hitmontop = Capoeira)
Smoochum: Baby Jynx
Magby: ? (I really doubt that it's a hadrosaur like WG suggests)
Blissey: Good mother/nurses and luck
Entei: Lion with some Newfoundland/Landseer mixed in.
Suicune: Looks somewhat like a shaved blue and white Afghan hound with a beard (Afghans sometimes have one) and enlongated purpled ears
Larvitar/Pupitar/Tyranitar: ? (WG: Dragons or dinosaurs of some sort?)
Lugia: Greek kingfisher god Halcyon? (there's a bird that looks like Lugia on the cover of Across the Nightingale Floor)
Ho-oh: Ho-Oh, the Japanese phoenix
Celebi: A forest fairy?
Treecko/Grovyle/Sceptile: Leaf-tailed geckos (Pokémon of the Day Chick thinks that Sceptile's tail looks like part of a juniper bush. I do, too. X) )
Torchic/Combusken/Blaziken: Chick and cockfighting chickens (Blaziken has some basis in the bantam rooster, and absol attacker suggested garuda)
Mudkip/Marshtomp/Swampert: Mudskippers/blue axolotls
Poochyena/Mightyena: Brown hyenas (Cub)
Zigzagoon: Raccoon dog
Wurmple, Silcoon/Cascoon: Horned caterpillar and luna moth pupae in the early stages
Beautifly: Old world swallowtail butterfly
Dustox: Female luna moth with some female 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
Nuzleaf/Shiftry: Konoha tengu
Taillow: Welcome swallow
Swellow: Barn swallow
Wingull: Gull, likely ring-billed
Ralts/Kirlia/Gardevoir: A tomboy, a ballerina, and a fairy tale princess/adult graceful woman dancer
Masquerain: Has some lanternfly and eye mimicry in it
Slaking: Ground sloth/gorilla
Nincada: Cicada nymph (the Pokémon Zoology page points out that Paras more correctly represents one)
Ninjask: Adult cicada/yellow jacket
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
Exploud: Pipe organ.... absol attacker thinks that there is also some howler monkey
Makuhita/Hariyama: Sumo wrestlers
Azurill: Unevolved Marill->mouse? (They were just working backwards.)
Skitty and Delcatty: Cats
Mawile: Bear trap
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.)
Plusle: Rodent/lagomorph+positive charge
Minun: Rodent/lagomorph+negative charge
Roselia: Rose bush
Carvanha: Red-bellied piranha
Sharpedo: Great white shark/ocean sunfish
Wailmer: Blue whale/ball
Wailord: Blue whale/basilosaurus
Numel: Dromedary (Arabian) camel/volcano (the two major types of camel)
Camerupt: Bactrian camel/volcano
Torkoal: Galapagos giant tortoise/coal
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?
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?)
Barboach: Loach/(mudfish [info]/mud-minnow)
Whiscash: Catfish (specifically the wels cat 1 2)
Baltoy: Shakou/spinning top
Lileep/Cradily: Coral polyps 1 2/crinoids (sea lilies)
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")
Castform: Cloud, weather conditions
Shuppet: A haunted tissue ghost
Banette: A haunted 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)
Wynaut: Small punching bag
Snorunt: A person wearing a straw blanket thing (pic from Zeta)
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
Clamperl: Giant clam
Huntail: Gulper Eel 1 2
Luvdisc: Discus fish
Bagon: Baby western dragon
Shelgon: Dragon cocoon?
Salamence: Adult western dragon
Beldum/Metang/Metagross: Sci-fi invader robots?
Regirock/Regice/Registeel: Jewish golems
Latias/Latios: Jet planes?
Kyogre/Groudon: An orca and an upright Desmatosuchus cast in roles similar to the Biblical Leviathan and Behemoth, respectively
Rayquaza: Eastern dragon (that looks somewhat like a lindworm)
Jirachi: Tanabata festival/genie (Jirachi has three green tanzaku on it)
Deoxys: Humanoid alien/mutated virus->DNA.... My brother thinks it looks like an orbital frame from Zone of the Enders.
Bonsly: Bonsai/petrified tree