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This is definitely more 'favourites' than 'best' or 'clever'.
Absol: Tai (from Taijitu, the name of the Yin-Yang symbol)
Altaria (shiny): Aultaria (shiny Altaria = gold = AU)
Farfetch'd (female): Miku
Glaceon: Nordlys (Norwegian for northern lights, was on winter cruise in Norway to see them when I hatched this little guy)
Leavanny: Arti (look, I hate the name Burgh)
Mamoswine: Babar (male) and Nellie (female)
Pansage, Panpour, and Pansear: Parsley, Peppermint, and Paprika
Salamence: Tatsubasa (from tatsu = dragon and tsubasa = wing)
Sawk: Argyle (I am genuinely proud of this one, okay)
Slaking and Vigoroth: Hulk and Hulkish
Tyranitar and Larvitar, both female: Myrtle and Minty
Vullaby: Tofurky I'm vegan
Fossil Pokemon: Got technical. Omanyte named Ammonite, Kabuto named Eurypterid, Aerodactyl named Pterosaur, Lileep named Crinoid, Anorith named Anomaloca (from Anomalocaris), Cranidos named Pachyceph (from Pachycephalosaurus), Shieldon named Ceratopsi, Tirtouga named Archelon, and an Archen I just got lazy with and named Archie, since Archaeopteryx is practically in the name already.
Gigantic Zelda set: HeartGold team that included Link the Meganium, Zelda the Espeon, Sheik the Umbreon, Morpha the Gyarados, Ordona the Ampharos, and Helmaroc the Ho-Oh, plus an HM slave Wooper named King Zora. Later editions include a Beartic named Telma, Torterra named Deku, Ponyta named Epona, Misdreavus named Midna, Clefable named Navi, male Unfezant named Ghirahim, Togepi named Cojiro (did actually originate in HG - it hatched from an egg), Axew named Nabooru (the axe she has as an Iron Knuckle), Magnemite named Scrapper, and Lilligant with Petal Dance, Quiver Dance, and Teeter Dance named Fi
