Here's my list based on the Zelda games I've finished.
1. The Wind Waker: I absolutely love this game. I think the cel-shaded graphics gave this game a unique look to it, and was a breath of fresh air from the "realistic" style. I know this game was criticized for it's sea travel (everyone said that it was boring and tedious), but it's one of my favorite aspects of this title. It made me feel as if I was really traveling across a whole new world instead of being confined to a small country. Plus it's the first (and possibly only) Zelda game to have free moving camera control.
2. Majora's Mask: I felt that this game was not only an improvement over OoT, but also a unique experience that stands out from the rest of the series. I love the NPC interactivity, the mask transformations, and Majora itself. In fact, I prefer Majora over Ganon/dorf. In my eyes, a villain who wants to destroy will always be more evil than a villain who wants to conquer.
3. Twilight Princess: I know gamers hated this game because it had almost no originality, but I think Nintendo wanted to keep the game play of this title similar to OoT because the elitists and fanboys complained about the other two 3D games being too different from OoT. However, I personally prefer this over OoT. I liked the combat system and sword techniques, the graphics (although WW will always be my favorite in this department), and the dungeons more than OoT. And the one thing that I absolutely loved about this game was Midna. She's cute, charming, funny, less annoying than Navi, and is my favorite character in the Zelda universe. This game met my expectations, and that's good enough for me.
4. The Minish Cap: To be honest, I'm not a fan of the 2D Zelda games. Yes, I have played Zelda I, II, Link to the Past, Link's Awakening, Oracle of Seasons, and Oracles of Ages, but I didn't enjoy them nearly as much as the 3D titles. However, I found this game to be not only the best of the 2D Zelda titles, but also better than OoT. I liked every aspect of this title. The graphics were good, the story was unique, the gameplay was excellent, the shrinking mechanic gave this game a whole new look, and the boss fights were great (especially Vaati). I think this game deserves every bit of credibility it gets.
5. Ocarina of Time: I'm probably going to get flamed for putting this one so low on my list, but I've just simply grown out of it. Yes, I do realize how revolutionary the game was to the 3D action-adventure genre and the gaming culture itself, but to me it matters which does it best, not which does it first, and I feel that every Zelda title that I've listed so far, and even other action-adventure games, were superior to this game one way or the other. Heck, I can't even recommend this game to new gamers anymore. But keep in mind that I do enjoy this game, just not as much I used to and not nearly as much as everyone else does.
6. Four Swords Adventure: Although I found this game to be fun, I also thought it was repetitive and I hated having to collect the little triangles over and over and over again.
Well that was my list. Now please keep in mind that I keep true to my own tastes and opinions, and that I'm entitled to them, just as much as everyone else is entitled to theirs. Sorry if I'm coming off as a over opinionated jerk, I'm just used to being bashed by Zelda fans in real life because I don't like Ocarina as much as they do.