1. Twilight Princess
2. Ocarina of Time
3. Majora's Mask
###. Majora's Mask
###. Skyward Sword
Bear in mind that I have not played hardly any of the 2D Zeldas - I think Four Swords Adventure(s?) is pretty much it. I will, however, say that there's no way I could possibly dislike them more than I do Skyward Sword, and probably Wind Waker as well. Wind Waker's visuals, as well as Skyward Sword's to a lesser degree, disgusted me. I also hated the whole sailing/flying thing both games have going on. Sailing was just a boring time-waster usually, while flying became painful because I hate motion controls and motion controls hate me - which basically sums up the rest of what I could say about Skyward Sword....except that Skyward Sword also had the most annoying sidekick out of all the games - and perhaps out of every game ever. And no dialogue skip, unlike Twilight Princess. And also, now that I think of it, a lot of the characters, especially in the beginning, were weird and/or annoying. Especially Zelda and Grouse + his gang. Grouse, admittedly, did get a little better, but that doesn't fix the rest of the game.
In reality, Wind Waker was mostly alright, (Skyward Sword was not), but it was a huge disappointment in comparison to either Ocarina of Time or Majora's Mask. When I first played Majora's Mask, I thought it was decent. Not great, but decent. When I played it through the second time, I really began to realize how much I didn't care for the game, and I only got to the Deku Tree on my third playthrough before I realized I now hated the game and quit.
Ocarina of Time, on the other hand, is probably the most solid game. Somewhat annoying companion, true, but everything else is pretty much great. Twilight Princess, while not being quite as solid as Ocarina of Time - sometimes, I felt as though the dungeon design was a bit...lacking, or at least not as much fun as Ocarina of Time's - gets my vote for favorite Zelda game simply because of its lovely companion. Majora's Mask is weird and somewhat different, but fun, so it goes above MM/SS.