Definitely Stone Tower Temple. One of the best in the entire franchise. My favorite part about it is that there is a really compelling story behind it. It's like that with all the dungeons, but not the way this one does it. I actually want to keep going so I can figure out WHY EVERYONE IS FRICKING DEAD. At the same time, the game keeps up this creepy, erie, and dangerous feeling throughout the whole saga! This makes you question whether you WANT to continue. But the key is the payoff, which is the dungeon itself.
Stone Tower Temple boasts a great soundtrack, it's riddled with enemies, filled with puzzles, and you even fight undead-fricking ninjas. Then you get a magic arrow that turns the entire temple upside down, so that the sky is below you. Then, once you make it past the puzzles and enemies, you get to the boss, where you put on a mask that turns you into a giant, then you start kicking ***. Stone Tower Temple is pretty doggone cool. By the way, spoiler.