5. Lanayru Mining Facility - I loved the look and feel of it, combined with the Time puzzles.
4. The Sandship - Same thing as above, only I like it more because it was slightly more challenging.
3. Earth Temple - Can anyone else sing the Indiana Jones theme?
2. Ancient Cistern - Creepy, but cool. Not to mention, Koloktos was the moment where Skyward Sword bosses stopped being awesome and started being straight-up kickass.
1. Sky Keep - Totally a dungeon, and awesome as hell. And you got to collect the Triforce. Nuff said.