I'm torn between Treeko and Mudkip, I used them both equally, but my last Ruby file I went Mudkip, so I chose that.
Same between Cyndaquil and Totodile, water again.
Squirtle for the majority of first generation, Charmander coming in second.
And Turtwig for D/P because everyone went Chimchar. I don't blame them, he's an amazing wallbreaker as a mixed sweeper.