The hardest dungeon in the series for me (out of what I've played) would probably be the water temple in Twilight Princess. It was'nt impossible, but throughout the entire dungeon, I had a lost and confused feeling, and no easy dungeon could give me the sense of accomplishment that this dungeon offered.
A close second would be Sky Keep from Skyward Sword. The rooms in the dungeon were relatively easy, but the whole moving around rooms thing always had me confused, and worried that I would make a mistake, putting a room in a bad place, and making it harder for me.
i think that the city in the sky temple from twilight princess is the hardest because the combat is thoroughly difficult, and i can't remember how many times i "fell to earth" so to speak. the hardest part of the city in the sky, was the puzzles. I usually take a few minutes to think things through as is, and it doesn't help with that horrible screeching music! I hate the city in the sky! that is all.
The hardest dungeon/temple for me would be the water temple in Oot. I just completed that yesterday and that dungeon took me at least 2hrs!? but those 2 hours were spread across days and months! XP i hated it because you have to go back to places that cannot be accessed before and get the correct level of water. bascially ALL of the treasure boxes was important coz you needed all of the keys and then the boss key. the boss stage was also really annoying and hard. it was a small piece of crap that u hav to try hookshot out and slash it. but u can like only slash it once coz then afterwards, it will jumpback into the water.
The Great Palace in Zelda II: The Adventure of Link. I got lost repeatedly in there and all of the enemies were tough. And then just when I thought I was finally at the end, along came the final bosses. "Bosses" since I would count both Thunderbird and Link's Shadow as bosses of the Great Palace, and either one is challenging enough on their own. I spent much longer on this dungeon than I did on any others in any game, and the idea of going back there has prevented me from trying to fully finish the game a second time. Maybe someday!
Ironically JabuJabu's Belly:
People allways told me the water temple was terrible, when I got to Jabu Jabu I was sure it was it, It was fun don't get me wrong, but I died CONSTATLY, not to mention a very bad headache from that Zora sitting on me, then when I got to the actuall water temple I found it wasn't all that hard, yeah switching boots was annoying, but that was fine, Like the topic btw dude
I think the hardest Zelda dungeon is the Water Temple in Ocarina of Time. It's really confusing with the different water levels and everything. The fight with Dark Link was hard, too. I liked the battle with Morpha, though.
The hardest temple was the water temple in Twilight Princess. It was very confusing with the stairs moving up and down and you had to go all over the place which annoyed me very much. Also the mid boss was annoying the tadpoles came at up with like 30s and you had to kill them so quickly to kill the mid boss. Also the dungeon was all in confusing and frustrating to me.