I think Majora's Mask is the best out of all the games (but I haven't played any of the gamecube games yet). A city where everyone lives their own (scripted) lives, the ability to transform into different forms, the three day time limit (with the option to go back to day 1) and the quest to get all the different masks... excellent design and gameplay. Nasty dungeons as well, it took me quite some time to finish it and I did need to peek at a gamefaq a few times because I was totally stuck...
The scene with the tree in the sunny meadow near the end... The best gfx I have yet to see in any N64 game.