For me, while Gen I, the original RBY, would still be my favorite, mainly due to sentimental reason, yet the game I probably enjoyed playing the most, at least on the handheld, would be RSE on the GBA, or more specifically, Pokémon Emerald, because for a Third game, you got to deal with two feuding teams, capture all three Legendary Pokémon in Hoenn in one game, and also served to fill the gap between RS and FRLG. Pokémon Colosseum would always be my top console game, because it not only served as a go between for the Gen III games, yet it was really unique in terms of storyline and approach, although the stealing the bad guy's pokemon in order to make things right makes things complicated. Stadium 1&2 were good games, especially with all the mini-games, and Snap was more lifelike, yet I liked them better then Battle Revolution.
Anyway, here is my list. Feel free to share, yet keep it clean, and as always Moderators welcomed to share theirs.