I believe it was The Sky City in Twilight Princess. It´s one of my favourite dungeons in all the Zelda games because of the boss: Argorock. I really LOVE dragons so it´s not so wierd that this is my favourite dungeon. My favourite element is wind as well so it´s quite obvious that I like this dungeon.
Woodfall Temple - The Legend of Zelda: Majora's Mask.
I got lucky during that fight. Odolwa cornered me so I kept jump attacking him and the game started glitching out. It let me repeatedly jump attack him until he died.