The Fire Temple, or Dongo-Dongo's Cavern. Both from OoT.
I've only been through two Wind Waker dungeons yet, so I can't really name a favourite there.
Skyward Sword has no favourite; I find the game frustrating, which is a thing I judge a dungeon on. I still like the game, but the dungeons are painfully puzzley.
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My avatar-Madison Gotha. She knows various weapons, she's a mage/sage, and is somewhat immortal. Madison has the capability of taming and communicating monsters, a genetic trait passed down by her father. 26 physically, 1400-something mentally, and a Lofty Peakian/Zenithian mix. Doesn't really like being called an elf and hates being called human..
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Mine is either the Earth Temple from Wind Waker, or the Thief's Hideout from A Link Between Worlds.
I've only been through two Wind Waker dungeons yet, so I can't really name a favourite there.
Skyward Sword has no favourite; I find the game frustrating, which is a thing I judge a dungeon on. I still like the game, but the dungeons are painfully puzzley.