"Most trouble with" is pretty vague.
Ocarina of Time, Water Temple- intellectually the most difficult one I ever did. I was 10, it was my first Zelda, and it was... well, it was the Water Temple.
Twilight Princesss, Sky Temple- most epically tedious dungeon I ever played. I LITERALLY fell asleep playing it. Passed out waiting for those idiotic slow-rotating clawshot platform/spinning paddles to come back around.
Stone Tower Temple, Majora's Mask- Not THE most difficult one I did, but there was a notable bit where I got stuck long enough I broke down and checked the Player's Guide... and it didn't help me at all. It glossed over how to get past the part I was stuck on. Which I'm actually glad for, because a short time later is when I had the random epiphany of where I needed to go, thanks to remembering how the iron gate moved in a cutscene.