To me, none quite compare than the Stone Tower from Majora's Mask.
For starters, it's got a really neat gimmick of flipping the entire world in the dungeon upside down, and also has an interesting music track that changes with it. The normal track is very somber but slightly uplifting, whereas the upside down version makes you feel like you're walking on a knife's edge or a tightrope.
Finally, the Twinmold bossfight is quite fun, especially in the remake where they gave you the option to hulk out on the boss.