It was so hard to decide. I loved the game and have beat it damn near a thousand times xP The water temple was frustrating due to the constant water level changes... and i loved the song in the fire temple, not to mention I loved the Gorons. x3 The whole game is amazing. I just seen on tv that the 3DS went down in price, so I may just buy it so I can get the game for DS instead of dusting off my N64 to play xD
I love them all to a degree and all for different reasons. I suppose if I HAD to choose, I would choose Spirit Temple. The boss is totally awesome. (And I always went out of order for Spirit and Shadow. *always went and beat Spirit first, then Shadow*)
Forest: It was amazing with the poes and all of the puzzles, and then phantom ganon FTW. Though I didn't particularly like the stupid wall masters >>;
Fire: I'm most in love with the song to teleport you there of all XD. Such a gorgeous song <3. The boss was awesome. Love dragons! But bleh on finding all of the gorons.
Water: The music of this temple was gorgeous, and I loved the idea of Dark Link as your shadow. I just hated how you always had to change the water level (because it was too difficult sometimes and I frustrate easily XD. Worst off, they continued that stupid idea in subsequent ones >>; )
Spirit: I hated the stupid wasteland. That was the main downside. Getting through that thing sucked >>;. I didn't care for the iron knuckle either >>;. And twinrova was a bitch XD. However, it had awesome music, and the idea of two witches joining to become one badass boss is nice.
Shadow: UGH. Just UGH. It scared me as a kid XDDDD. It was that...that THING. The Deathhand >>;. That thing scared me the most. Hoverboots FTW <3. It was just a challenge because of all of the traps and the boss, Bongo Bongo...bleh XD.
I picked the water temple, but it was between that and Spirit. Spirit lost because I don't like having to be a kid, and because one of my favourite things about it is that it reminds me of the Light Forge from Soul Reaver 2.
So Water Temple is my favourite, even though...fucking shoot me, you know? But whatever. It's a well-designed, challenging temple that frustrated the hell out of me and had the most difficult sub boss (arguably one of the most difficult bosses period) in the game, and that's what I love about it. It's hard.