Ancient Cistern (Skyward Sword):
Just hauntingly beautiful, the entire dungeon was really well made, and Koloktos is easily one of the best bosses in the series. This could explain more than I could:
http://www.zeldadungeon.net/2012/01/...cient-cistern/
Forest Temple (OOT):
Atmosphere is top notch, it's dark, and really creepy. I think they really achieved what they wanted with the music, and the over tone throughout the entirety of it.
Stone Tower Temple (Majora's Mask):
Honestly.. I love the music, a lot. It's probably the only reason it's being listed. Probably one of my favorite tracks in the entire series, somewhere after Dark World.
A runner up would be the Sand Ship from Skyward Sword, just.. mecha pirates, I really enjoyed it a lot.
As for least favorites,
Water Temple (OOT):
It is SO easy to screw this up, I think there was even a way in the original game to completely fuck your entire save file over by using the wrong key on the wrong door. To this day, I STILL get lost in here.
Water Temple (MM): This is kind of a huge hurdle in replaying MM for me, I love the game, I really do, but the pre events following it, and the temple itself, just quickly turn me off. :<
Water Temple (TP): Yep, all 3. Annoying as fuck water raising stuff, just.. everything that makes all of these temples a huge pain in the ass.