Ganon's Tower was definitely fun, facing old bosses again with updated music... that was neat. I preferred the Wind Temple and The Forsaken Fortress #2.
The Wind Temple was one of the more challenging dungeons, had a really fun boss and mini-boss, and I felt so relieved to get the Hookshot. The Forsaken Fortress #2 was awesome because of Phantom Ganon mostly, but I really loved being able to slaughter some of the bastards that kept locking me up the first time, lol. I also liked fighting the Helmaroc King, as I wanted to since the beginning of the game, and he looks really cool. The Skull Hammer is also the best upgrade from the Megaton Hammer, which was way to small to use effectively in combat.
I think the Forbidden Woods deserves a mention as that is my favorite Boomerang themed dungeon in the entire series (so far), it was extremely fun to use and I am a big fan of those style bosses. The Deku Leaf was also quite a fun tool to use as well, not just in the Forbidden Woods but throughout the game.