I actually like all of the dungeon music within the game. However, if I had to choose, it'd probably be between the Spirit and Forest temple's music. The Spirit Temple gives a nice, fitting sound that makes you feel like you're actually in something that's located in a desert. It also just sounds great to me.
However, the Forest Temple is creepy, eerie, and just works really well. It almost makes the place feel like anything could jump out and attack you, it actually creeps me out more than the Shadow Temple, which is one of the reasons I like it so much. It just has this feeling of mystery within the music, which helps the temple its self have a lot more atmosphere, which really adds to it.
So between the Forest and Spirit Temple, I'll have to go with Forest, mainly because I like how the music fits the area, which makes it sound better to me. Also because I generally like the creepy sound to it without it actually aiming to be a creepy track, like the Shadow Temple's music.