I personally love all the temples from both Ocarina of Time and Majora's Mask. And as much as I try to remember Wind Waker ones, I just can't.

If I had to choose a favorite, Forst Temple from OoT, it had a mystical and creepy enviroment none else had, not to mention, the characters and enemies. And the last one from Majora's, the whole turning upside down, and the way you had to go through to get to the temple, just kickass.