I have to say Majora's Mask. I loved OoT, but there were so many aspects of MM that I fell in love with even more.
First off, there was all the masks and especially, the transformations. Even the non-transformation masks tended to have powers or just look cool.
The story is another big thing. I've heard people say they wanted a deeper storyline, and while it wasn't right there in front of you all the time, MM had it. If you pay attention, the characters were actually really deep, and there was a lot going on, most of it intertwined with other events in the game.
The time system was brilliant. It was amazing how everything was worked out, and how the uniqueness of that addition affected the game so much.
The style. It was darker, yeah, but in a brilliant and in some cases, beautiful way. Everything was so interesting, and while some bad stuff happened to characters, it was worked out by the end of the game. I really don't think Zelda should get darker than MM, and that's the main reason I dislike Twilight Princess.
And finally, the design. The whole game was worked out so well. The puzzles and quests were elaborate and unique. Some of this was the time system; it gave the game designers options that other games don't have. But at the same time, other aspects weren't well designed because of the time system. An example is the dungeon design. The dungeons were amazing.
Anyway, end geek rant. I just love Majora's Mask, it's definitely my favorite Zelda game.