I have so many.

OoT
Forest Temple because of the music.
Shadow Temple because of the invisible stuff
Spirit Temple because of the need to time travel

WW
Forsaken Fortress because so much of the story goes on there, stealth and Phantom Ganon battle music is awesome.
Earth Temple because flying Medli was fun, and because of the mirrors.

TP
Arbeiters Grounds because the battle with Stallord on the spinner was so fun.
City in the Sky because it's a city. In the sky.
The mansion with the Yetis, I can't remember the name because it was just... fun.
Temple of Time because it's the Temple of Time AND it's similar to Tower of the Gods in WW.