The hardest dungeon I've played thus far is probably the water temple from Twilight Princess because I thought it was really confusing having to change the stairs all the time. It might be becaus I was very little the first time I played Twilight Princess and I've only played it once...
The hardest or me was the Water Temple in OOT. OOT was the first Zelda game I played and I walked into a doozy. I just remember rage quitting several times and refusing to look for any walkthroughs. I stuck with it though and the sense of accomplishment was one of the most satisfying things that I had experienced in a long time. It taught me to stick with things even when they are super difficult and to look at things from all angles in order to solve problems! And they say video games don't help in real life.
The Eastern Palace from the Legend of Zelda: A Link to the Past was the hardest dungeon for me, mostly because the difficulty level in the Link to the Past dungeons is much greater than other Zelda games I had played so far, such as The Wind Waker, Twilight Princess and the great and honorable Ocarina of Time. The dungeon boss, the Armos Knights, was also a challenge because I felt it was hard to maneuver around that tiny room and get a good shooting angle with my Bow. I felt very proud once I conquered it.
The forest temple from ocarina of time was actually the hardest for me. I got lost so many times because I'm not good at dungeons that have a central hub area and different sections that lead off of it.
The hardest temple for me was the water temple in OoT, i kept getting confused with everythng. No matter how many times i go back and play over that temple i still cant remember where the keys are at XP
Any water / ice temple / dungeon realy but the hardest one i played was in Oot . It was so easy to miss the small keys and it took me 4 days to complete it . I didnt like having to raise and lower the water all the time and it was a hasstle to keep equiping and unequiping the iron boots .