Majora's Mask for me. Though Wind Waker does reserve a special place in my heart because of its music.
I'm actually in the middle of my 7th play through of Majora's Mask since it came out. Granted its not near as difficult anymore (due to the fact that I'm 19 now, and that it's my 7th playthrough lol). I think I like this one for what someone else said, no regular Zelda bullshit is a part of the story. It is an original idea as far as its story goes. There are also a lot of eerie moments in Majora's Mask that will be forever engrained in my mind, such as the Ranch battle against the aliens, the surreal field where you find 5 children wearing 5 different masks each representing the bosses defeated and to be defeated, and the sheer desperation each area is under because of the Skull Kid/Majora's...antics, for lack of a better word
Twilight Princess I liked, and thoroughly enjoyed, but its a been there done that kind of story, except for the wolf thing, which was quite interesting.
OoT was good, and it actually was the first Zelda for me, and I have played through it about 3 times, but Majora's Mask will always be my favorite game