If the Fire Temple music you're referring to is the original Fire Temple music, then that one is my favorite. I dunno, I just love the Islamic chants they put in. They add to the atmosphere and go along well with the temple. If that's not included then I would pick Forest Temple, which was very creepy and went along very well with the atmosphere of the temple.
Aw, man, all these songs sound awesome, it's so hard to choose only one. They each have a melody and sound that perfectly matches the temple that they're representing. But since I have to choose one, I think the Water Temple's song is my favorite out of them all. I like how it sounds like both water and ice at the same time which is kinda funny in that the water temple's symbol was originally going to represent ice.
The Forest Temple soundtrack is really impressive, actually scaring me a bit the first time I played through it, while the Shadow Temple music did nothing to me... It gives the temple a mysterious feel, and you just have to love it. Simple as that. Love it. LOVE IT. L-O-V-E I-T.
The Fire Temple music is the most boring for me, no offense to anyone. Strangely, it's the only soundtrack appropiated to a temple where people goes to pray to someone, or that kind of things. Still, I like it, though it is my least favorite soundtrack out of the five temple soundtracks.
The Water Temple soundtrack I do really like, it fits the water theme perfectly, and it is pretty much my favorite soundtrack with the Forest Temple one. Got to love it as much as the Forest Temple one.
The Shadow Temple soundtrack is quite interesting, especially as the boss itself interacts with it (bongo Bogno is the one who... well, plays the bongos in the song XP). I find it quite amusing, I like it very much, but it is a bit poor if you count it as a soundtrack, as, in my opinion, it isn't really a soundtrack, just something else it's name I can't find.
The Spirit Temple is like being inside a pyramid, beig mysterious and a great soundtrack, really great, being my second favorite, and the one that fits the most with its theme, maybe even more than the Water Temple soundtrack.
Well, Forest Temple soundtrack, Water Temple soundtrack...
The Forest Temple just because it is a bit less calm than the other soundtrack.