Stone Tower Temple, Deku Palace, Woodfall Temple, Song of Healing, Elegy of Emptiness, Clock Town, Astral Observatory, Termina Field, the Clock Tower... I love so many tracks in the game. I couldn't possibly list them all--or better yet, just say the entire OST. I would have to say my favorites are the ones I stated, though.
I really like the piano version of the Song of Healing is one of my favorites because it really enhances the sad and apocalyptic atmosphere. I also like the Oath of Order at the top of the Clock Tower and the upside-down version of the Stone Tower Temple theme.