Without a trace of doubt:

I'm gonna somewhat copy smeags:

Gen I: Charizard

Gen II:Espeon

Gen III:Blaziken

Gen IV:Palkia

Gen V: Haxorus(though Zekrom is a close 2nd)

Said it in trasharm's thread, and I'll say it again.

Gengar will fuck your shit up.

Haven't played any mainline Pokémon games that weren't on the original Game Boy, though, but I doubt I'd change my mind if I had.

*points at avatar*

No matter how awesome any new Pokemon might be, I'm gonna have my bit of nostalgic bias, :D.

Charmander/Squirtle/Bubasaur

ITS SOOOOOOOOOOOO HARD TO CHOICE 1!

I've always been partial to Flareon. Plus he has MASSIVE attack and special in Gen 1. 

Dragonite, Obviously. Although i must say i love squirtle.

this you should have seen how exited I was when I found someone on a bridge in pokemon white willing to sell one for just 500!!!! I would have payed 50,000 easy