Choose just one? Impossible.
Few have mentioned the Hyrule Castle theme in Twilight Princess yet, likely because it's a remix of two songs from Link to the Past. Still it's wonderfully atmospheric and builds as you get closer to the top. Would be even more effective if the castle was longer/more challenging IMO (would have 4 or 5 tiers instead of 3, much like Final Fantasy's 'Dancing Mad'). Come to think of it, put all the music from Twilight Princess' finale up here.
Speaking of undermentioned songs, I doubt the Game Boy ones will get much credit due to differences in sound quality, but the Dancing Dragon Dungeon in Oracle of Seasons is extremely catchy, same for Moonlit Cavern in Oracle of Ages.