I will admit that my Zelda experience is somewhat limited, and that my answer is rather typical, though maybe for an atypical reason. The hardest dungeon I have experienced is the Water Temple from OoT. Now here's the atypical reason: the Water Temple's difficulty scales up if you have to quit and resume multiple times while figuring it out. When I first played OoT, I was still in elementary school and had to follow my parents' rules for daily game time. As a result, long dungeons were multiple-day events for me. (And don't say I could just turn the TV off and leave the N64 on: I have a brother that used it, too.) While this added a new element to most of the dungeons, the Water Temple was most affected by it, due to trying to remember overnight which water level I needed and how to get to wherever I was from the beginning of the temple. At least once I needed to change the level twice just to get back to where I was the night before.