For me, the hardest dungeon has to be Stone Tower Temple from Majora's Mask. It was so complex and difficult, but also interesting and fun to think out and think about and think about how I could do something differently. It was a really hard dungeon.
Honorable Mentions: The Water Temple; Ocarina of Time, The Cave of Ordeals; Twilight Princess, Death Mountain; The Legend of Zelda.
-crosses fingers-