I get lost and frustrated in there plenty, but it's my favourite Temple for the sole fact that it features Dark Link as a mini boss. That fight is one of my all-time favourites of the game and I always look forward to the Water Temple because of it.
I love the Spirit Temple (you mightve guessed that if you looked at my name) the boss was hard, but lots of fun for me. I love how you have to travel through time and do the temple as a child and as an adult. I like the Mirror Shield too. The Iron Knuckles made a nice change to regular enemies and I enjoyed fighting them. They Anubis puzzle . . . well, puzzled . . . me at first but it was really cool how it was designed and how you had to figure it out (I loved it despite the fact that I fell off the edge numerous times forgetting that the floor wasnt there while I was trying to get them in the right place). If I was to pick a second favorite, it would be the Water Temple, however much it drove me crazy (but I thought Dark Link was a heck of a lot harder than the actual boss, which was very strange, but I guess it wouldve been easier if I had gotten the Biggoron Sword before then).
Well, not neccessarily.... You needed it 4 Ganon at the end so you could hit his tail with lotsa light arrows also....
My favorite is Ganon's Castle. It has all the temples in one HUGE building. You know?