The Water Temple from Ocarina of Time. I know that when I was young that is the only temple that caused me to "shelf" the game for a long period of time. It is the only dungeon to have done that to me.
To me the most difficult dungeon was Turtle Rock from Link's Awakening. Mostly because it was so big, and there were a lot of things that could be done at the same time, so I forgot about some of them and was stuck for a while. And the mini boss of the dungeon, Blaino, was very cool, but really annoying when he knocked me back to the entrance of the dungeon about three times...
Personally I'm not a big fan of the Great Bay Temple from Majora's Mask. It was pretty difficult the first time, and still is. I remember playing it during the CD - I live event, and having people in the chat help me, and having ZD open, for the stray fairies.
That cursed Water Temple... i shudder thinking about it! I always seem to go through one of the tunnels and get lost, or finally find the dorr i need and dont have the Small Key to open it. I always fall in the water fighting the Boss, too. Ugh... not to mention those clams, they always snap shut just as i pull out my hookshot!
The Great Bay temple in Majora's Mask was the hardest dungeon (for me at least). Gyorg just took me so god damned long, and the gears! oh the gears! Water levels and aaaaaaaaaaaaaah I just can't even think of how long that dungeon took me to complete!
my the hardest zelda dungeon was probably the last tower pf sprits from spirit tracks. It was so frustrating not knowing what to do and you also had be stealthy or else you were going to get killed by the guards. it really gave me a hard time.
The hardst one for me, the one that made me throw my controller at the TV, would you believe, was the 9th dungeron in the original legend of zelda (2nd QUEST), you don't know how frustrated I was with all the hidden walls and bombing and then getting lost many many times.
Well, of the ones I've actually PLAYED, I would have to say Snowhead Temple from Majora's Mask. I found the set up to be VERY confusing, and I was just overall bad with Goron Link's controls. I kept getting lost and confused throughout the entire friggin' thing... And I just hate ice temples in general, with all the 'freezing' business... BLARG
I think that the Water Temple in the Ocarina of Time was one of the most annoying/challenging dungeons. I simply despised it lolz. The only plus side to the dungeon for me was the fact that you were able to engage into battle with Dark Link halfway into it. I thought it was an awesome way to give a nod to a classic game from the past. The many whirlpools throughout the water you had to avoid, hookshot skills, timing, etc. Morpha ( the final boss) made me want to pull my hair out at times. It moved around so quickly that if you made one wrong shot with the Hookshot and did not hit the 'nucleus' part that you had 0 chance until it came around again. Also, (maybe I'm just thoroughly dumb..which could be the case heh) when I would z-target it I found myself falling into the water 9 times out of 10 trying to reach the boss. I was so happy when I never had to step foot back in that place again.
The hardest dungeon is definitely the Great Bay Temple from The Legend of Zelda: Majora's Mask. The navigation throughout the opposing currents and changing them was very difficult. At first defeating the boss was a pain in the ***, but after many times of playing it I got use to beating it. The layout of the map is highly confusing as well, definitely a fun challenge
Since I've played Zelda II, all dungeons from all other games automatically go out the window. Probably the one that I had the hardest time with was the Hidden Palace. Objectively speaking, the Great Palace was probably harder, but it had the major advantage that if you died, you could start over again right at the start of the dungeon. With the Hidden Palace, it was a dangerous trek just to get back to the dungeon. Plus the first time I played through the game I was still having a hard time with the blue iron knuckles at that point.
The hardest dungeon in my opinion was the Lanayru Mining Facility from Skyward sword. This was really challenging for me because it introduced lots of new puzzles and it was really long. Plus the time-shift stones in the dungeon were really hard to find and it took me about 5 hours to get trough the dungeon with no help. Also and finally I died about 10 times in this dungeon.