For me it's either the Tower of the Gods from Windwaker or Snowpeak Ruins from Twilight Princess. The former has better puzzles and overall layout and design but the latter Is great for it's unique theme and weapon.

I have to say, I really enjoyed that second forest dungeon from Skyward Sword. The lotus motif, the gold everywhere, that underground section with the zombies, and a hell of a fun boss fight to top it off. If it counts, though, I think my favorite section from any Zelda game was in Wind Waker, when you get the Master Sword and storm Ganon's fortress. It ends up not really being all that effective, but getting your allies to help out and having a dragon blast the dude in the face while you make your escape was fantastic.

It's really hard for me to think over all of the dungeons I've played through; but the one that immediately springs to mind is Palace of Winds from Minish Cap. The boss battle was especially memorable.

Water Temple - The Legend of Zelda: Ocarina of Time 3D.

Oh that's tough.
 
Probably one from A Link to the Past, loved those.

@awadnin said:

Water Temple - The Legend of Zelda: Ocarina of Time 3D.

it's like an abusive relationship. been treating you like shit for years but then it sobers up, says I'm sorry and gives you a foot massage and you're falling head over heels in love with it :D

seriously though, that dungeon gets way too much hate. the dungeon itself has never been bad, it was just the tiring back-and-forth between the menu to put on those damn boots.

as for myself ... this is a hard one since I hardly remember any by name and I have played most games only once many years ago.

What sticks out is the Forsaken Fortress from Wind Waker because ... well stealth! That concept was completely foreign and new to me at the time.

Skyward Sword's Lanayru Mining Facility also comes to mind because the setting itself was just so different ... technology. Wow! And the whole time-mechanic thing? Pretty cool! And that Skyloft dungeon at the end ....!

Similarly awesome was the snow dungeon in Twilight Princess, that whole story surrounding the place was awesome! Oh and the Goron dungeon because hanging upside down and blasting fools with arrows is as gangsta as it gets :P

I wish I could name one from the 2D games but they all mesh together for some reason ... even though Link to the Past is my favorite Zelda game, I cannot name one dungeon that I'd call truly awesome or better than the others.

But maybe the mine-cart dungeon after you get the mole mitts from Minish Cap .. I love riding in mine carts :D

The shadow temple from Ocarina of Time. Creeped the hell out of me when I was a kid.

That's a tough one. It's a toss-up between Snowpeak Ruins and City in the Sky from Twilight Princess.

I fucking love the music in the forest temple.

OoT Fire Temple or the Spirit Temple.

For me it was always either Thieves town,Turtle Rock or Gannon's tower off ALTTP.

@Dalai said:

and City in the Sky from Twilight Princess.

oh right! I loved using the clawshot in TP ... well until I got stuck because I neglected to actually look UP at that one point :)

Shadow or Spirit Temple from Ocarina of Time

I liked that boat one in Skyward Sword, a very different setting, also slightly less linear than the others in that game.

I have not played every Legend of Zelda, so I don't really qualify. But from the games i have played, I'd choose the pirate ship from Skyward Sword. The boss was cool, and it just felt unique. Also, you finally get the bow, which was a bonus. The only dungeon that could compete with that is Forsaken Fortress from Wind Waker. I loved the use of stealth. The only downside was that is was short.

While Twilight Princess is commonly seen as one of the worse Zelda games. I think it has some of the best dungeons in the series. Specifically the second half with City in the Sky being a cool new departure, Arbiters Grounds, Snowpeak Ruins, and the awesome mini end dungeon in Hyrule Castle. Also the Temple of Time was col too.

It was a long time ago, but I remember that one in Majora's Mask that you flipped upside-down being pretty cool.

The sky one in TP.

That upside down tower from Majoras Mask

@yoshimitz707 said:

The sky one in TP.

City in the Sky. Yeah that one was awesome.

Sky Keep is far and away my favorite!

I really liked the final dungeon in Skyward Sword, where you shuffled the rooms around like a slide puzzle, although that could just be because it's so fresh in my memory.

The Manji:

All of A Link to the Past

I really enjoyed the last dungeon from Skyward Sword. The slide puzzle aspect was really different.

Edit: Sky Keep, yeah.

definitely stone tower temple in majora's mask. best music too

@ZOnikJJ: @FreakAche: @sonicrift: You three are insane. That dungeon has the potential to doing something unique but opted to reuse the same aesthetics and puzzles designs the rest of the game went to three times over. I dislike slide puzzles so the dungeon in one was frustrating for me. At least the other puzzles were enjoyable to solve.

I really enjoyed playing through Ancient Cistern in Skyward Sword.

I really enjoyed playing through Ancient Cistern in Skyward Sword.

@ImmortalSaiyan said:

@ZOnikJJ: @FreakAche: @sonicrift: You three are insane. That dungeon has the potential to doing something unique but opted to reuse the same aesthetics and puzzles designs the rest of the game went to three times over. I dislike slide puzzles so the dungeon in one was frustrating for me. At least the other puzzles were enjoyable to solve.

The mechanics in each room were unique enough for me. I liked that they used the aesthetics from different parts of the game since it reminded me of the past areas.

@ImmortalSaiyan: Well if you don't like slide puzzles, I can understand your issues with it, but if you're taking issue with the recycled aesthetics, that's something that the final dungeons in Zelda games have been doing for a while now. The final dungeon always features rooms evocative of each of the previous locations.