I'd probably rate Ocarina of Time higher, personally, if it weren't for the too happy attitude and gaping plot holes. I like a heavy dose of melancholy in Zelda games, so my top three, in no particular order, are Link's Awakening, Majora's Mask, and A Link to the Past. The time travel aspect prevented any of the unhappy happenings in Ocarina from feeling permanent or like I had a direct hand in changing them. Contrast that to Majora's Mask, in which a large part of the game was fixing everything that was wrong, including saving the world from impending doom, or Link's Awakening, in which you had to destroy the island and everyone living on it in order to escape.
Wind Waker is somewhere in between. It has a happy-go-lucky attitude about it for the most part, but it also has doom on a grand scale. There's a sense that the entire world is diminished. Ganon's speech is a great example. The game is also incredibly stylish, with excellent cinematic scenes and some tremendously exciting moments, including some great boss battles (though I must say that Ocarina had my favorite boss battles so far).
One of the reasons I'm looking forward to Twilight Princess so much is because it looks like it's going to be chock full of the melancholy attitude I like so much. There's a beautiful sadness in the graphics that I can't really explain. Not to mention the Twilight itself. That's nothing if not suggestive of ending and loss.