Three favorites: (WARNING all Zelda games!)
1. Ocarina of Time, I have a copy for N64, the masterquest disc, the collector's edition copy, and the 3DS version.
2. Twilight Princess, Gamecube version, my much preferred version of the game. I have the Wii version, but I haven't played it since I got the Gamecube version.
3. Majora's Mask, have it for N64, collector's edition version, and got it on Wii virtual console.
Least Favorites:
1. MLB game for N64, my brother loved baseball back in the day, so he liked baseball games, I didn't.
2. MLB game for Gamecube
3. Random Spongebob game for Gameboy Advance(I don't even remember the name), though Battle for Bikini Bottom for Gamecube is still pretty good for a licensed game.