Strangely enough the dungeons from the 2D-Zeldas kinda meld together in my mind, I remember bits and pieces and the general "feel" of each game, but there's no singular dungeon I would call the best. For the 3D-ones:
- Ocarina of Time: They're all quite great and have a nice progression. I tend to get a bit annoyed at Lord Yabu Yabu, it's manageable though. I actually like the Water Temple, it has it's share of flaws, but it's cleverly done and uses its theme well, unlike let's say in a game like Skies of Arcadia. My favorite is the probably the Desert Temple, though I'm also partial to the Shadow Temple and the Gerudo Fortress (including the Gerudo Proving Grounds).
- Majora's Mask: Overall my favorite selection of dungeons in the whole series, quality instead of quantity. The final Stone Temple is the best, and again I think the Water Temple gets a bad rap, it's very well made. Oh, and the Gerudo Fort may be only a small bonus dungeon, but I like it a lot.
- Wind Waker: Dungeon-wise the most disappointing 3D-Zelda, at least for me. It has it's moments, but you can really feel that the developers probably didn't have enough development time and the complexity was toned down. The first stealth passage is the most tedious dungeon in the series, there's a re-used boss from OoT and some dungeons seem to have been cut entirely. As I said, the dungeons have their moments, but it's not for me. Love the artstyle, btw.
- Twilight Princess: A return to form, in my opinion. The first dungeons feel a bit plain and rehashed, but the game keeps on raising the bar with great new items (magnetic boots, spinner) and culminates in the City in the Sky, I love the double-hookshot. I remember not being to fond of the wolf-sections, but I'll replay the game one of these days to solidify my opinion.
- Skyward Sword: It's a bit tough to judge the dungeons on their own merit, because the "overworld" is now a kind of dungeon itself. The actual dungeons are a bit smaller because of that, especially in the beginning, but they bounce back very nicely towards the end. The "time ball" is such a brilliant idea and well implemented, dungeons like the Ancient Cistern, the Desert Ship and hidden one in Skyloft are among the best of the series. Some ideas like flooding the forest are great as well, but the execution is lacking.
EDIT: Didn't play enough of Phantom Hourglass and Spirit Tracks to judge them fairly.
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It was the Zelda Dungeon I ever completed, and the boss fight was so fun.
