I don't even need to put any thought into this. Stone Tower Temple, man! :xd:
It's actually my favorite dungeon out of the entire series. It had an awesome song, great atmosphere, awesome enemies, great puzzles, was really hard, innovative concepts, cool boss... the list goes on.
It also really expanded on the whole Ikana theme, all the tortured undead and evil curses. It was so haunting, mysterious and disturbing. That's what I loved about it. It was also the game's "undead dungeon" and yet it never relied on undead themes, more on evil, and it kept things interesting. Love it! <3