I'll state what I thought was the toughest dungeon from each game.
Legend of Zelda - Death Mountain (Level 9) - This place was big, confusing, had many returning bosses, and you had to place a lot of random bombs.
Adventure of Link - Great Palace - I haven't gotten a chance to play AoL myself, but this is what I commonly see as the hardest dungeon in AoL.
A Link to the Past – Ganon’s Tower – This dungeon was twice the size of the regular dungeons in ALttP, had three returning bosses, many hard enemies, and a decently tough boss fight.
Link’s Awakening – Turtle Rock – This dungeon was bigger compared to the other ones, had several mini-bosses, and many good puzzles.
Ocarina of Time – Water Temple – Commonly accepted, but I thought that the switching of the water level several times was confusing.
Majora’s Mask – Stone Tower Temple – This dungeon was hard as it made use of all the transformation masks instead of focusing on one, like the other dungeons.
Oracle of Seasons - Explorer’s Crypt – It was bigger than the other dungeons, including the final dungeon, and the several floors component in it made it confusing.
Oracle of Ages – Jabu-Jabu’s Belly – This dungeon took me ages. The different water levels and good puzzles in this dungeon made it hard.
The Wind Waker – Wind Temple – I didn’t find any of the dungeons in this game to be hard, but this would be the one I choose, just because I thought the puzzle were a bit harder than in other dungeons in this game.
The Minish Cap – Palace of the Winds – This dungeon was huge! I thought it was over when I first opened the boss door, but it wasn’t a boss door! It also contained harder enemies, and a pretty hard boss fight. I also liked the interactions between the first and second part of the dungeons (like pressing a switch to make a key fall in the first part, then collecting the key in the second part), which nearly made me forget to collect the key!
Twilight Princess – City in the Sky – The Lakebed Temple came close, but this was harder for me, because of its several floors, which made it confusing.
I haven’t played Phantom Hourglass or Spirit Tracks either.