Can the natural silence that accompanies the overworld count? The silence can be the most beautiful track in the game, depending on where you are.
Demise of the Ritual, the soundtrack for Malus, deserves special consideration as a good example of making sure the music matches the tone you trying to be conveyed.
Gate Watcher of the Castle Ruins, the boss theme for the penultimate Colossus. Certainly fits the mood of the fight, considering how long figuring out how to beat that colossus takes.