I voted for Ocarina of Time, but then right after I hit submit I changed my mind. I would choose a tie between Ocarina of Time and Twilight Princess. My first game into the series was Ocarina of Time and I loved it. The dungeons were hard (way back then), the bosses were big and interesting, the game took a long time to complete, good music, atmosphere, and story. I just loved it.
A little while after Majorah's mask came out, my brother and I rented it and I watched him play it. He was always better at games than me, and I wasn't too good at those games back in the day, so I was content with just watching him beat it. Well, he beat all the dungeons and then got bored with it and never beat the last boss, despite having a day or two before having to return the game. I never did rent it again or buy it for cheap, so I can't really say much.
My sister bought Wind Waker. She must have beaten that game with 100% completed several times by now. I watched her play parts of it, but I never picked it up due to what I say as excessive sailing and the color scheme. I don't mind cell shaded games, but the colors for that game made me nauseous just looking at it.
I played Twilight Princess a year ago and absolutely loved it. Everything about it; the story, the pacing, the world and environments, atmosphere for the dungeons, the dungeons, and the bosses. Even though the bosses were easy, I still loved them. I've probably beaten the game 3 or 4 times. I thought the change to the wolf form was a great change of pace and the instant warp to several areas in the late part of the game helped reduce the monotony of travel found in other games. So while I absolutely loved Twilight Princess, I just wish the bosses were more challenging.
I guess I can't really compare much, because I haven't played many games out of the series, but I think I'm going to pick up Majorah's Mask some day and work myself through Wind Waker, who knows I may end up liking it.