Gerudo Valley ~ It's just so epic. It feels very dangerous. Obviously because when you first enter the area, you have to sneak through the fortress.
Epona's Song ~ A very relaxing tune (except for Malon's singing, which, due to the low-quality "voice", sounds like MIDI agony).
Serenade of Water ~ Again, very relaxing. Try playing it at night in Hyrule Field (as an adult, of course) next to the Zora River so you can hear the water running.
Bolero of Fire ~ It's just awesome. I don't know why. Perhaps because it sounds very passionate.
Sheik's Theme ~ Fits his/her character perfectly. The melodic, yet slightly disjointed harp complements Sheik's odd, poetic speeches.
Fire Temple (version 1.0) ~ The chanting makes it sound very mysterious.
Spirit Temple ~ Like the Fire Temple, had a mystical, sacred feel to it.
Zelda's Lullaby ~ Need I say more?