My favorite is the Requiem of Spirit. The Spirit Temple is also my favorite dungeon in OoT, and I think it really adds mystique to the whole desert theme. Ees ah beeeeuty of ah sawng.
Honorable mentions go out to the Nocturne of Shadow and Prelude of Light. The NoS was creppy, tranquil, and terrifying all at the same time. I love the cutscene when you learn it from Sheik. Very interesting...
The Prelude of Light is very nice, as well. Besides being the most used song in the game, it just epitimized the theme of the ocarina. It sounded like light. The tune, I mean.
I honestly liked all the songs. I also give props to the Serenade of Water. That was Rutela's theme from TP, and I thought it suited both purposes perfectly. So, although I like them all, my order would have to be:
1. Requiem of Spirit
2. Nocturne of Shadow
3. Prelude of Light
4. Serenade of Water
5. Bolero of Fire
6. Minuet of Forest