Charmander in Red, Chikorita in Silver, Gold & Crystal, Torchic in Sapphire & Emerald, and Charmander again in Fire Red. (I absolutely love Charmander!)
As you can see, I've picked the first Pokemon I started with in each region. That doesn't mean I haven't got every version, I just picked the Pokemon I first got off the generation.
I had Squirtle in Red (though I restarted later to get a Charmander), Chikorita (strangely enough o.o) in Silver, Totodile AND Cyndaquil in Crystal (I restarted the game a lot and used both of them), Charmander in FireRed and LeafGreen, and Treecko in Ruby, Sapphire, and Emerald.
Pikachu in Yellow, Totodile in Gold, Totodile in Crystal, all in second Crystal file (traded eggs over), Treecko in Sapphire, Torchic and Mudkip in Emerald (again, traded over), Charmander in FireRed, Bayleef in Colosseum.
Pikachu is Yellow, obviously
Shiny Totodile in Silver (I didn't even know it was Shiny at the time!)
Chicorita in Gold
Cyndaquil in my other Silver
Cyndaquil in Crystal
Charmander in Blue
Quilava in Colloseum
If I had any of the third generation GBA games, I'd have chosen Treecko, though.
Bulbasaur in Red, *female* Cyndaquil in Silver, Chikorita in Crystal, Treecko in Emerald. Will SO get a female Quilava in Colosseum. I want my Kazan-hime back T_T *cries*