OK, obviously the most underrated songs are those which you get to hear very rarely and are very good however:
- I also have to say Zelda's theme from aLttP, because you get to hear it only once and only for a short time, that's why many people don't know that the 2nd part of the song as heard in OoT was already there in aLttP because when you get the crystals, only the first part of the song plays and repeats. IMO they should have played the full song when you rescue Zelda from Turtle Rock.
- Ending themes in general, especially those of aLttP and MM.
- Another song that is rarely noticed plays in TP when you go back to Ordon Village at a certain point in the game, when the children are captured. It's often missed because you don't have to go back to the village at that point (it's actually quite a detour). Note that when you go there as a wolf to get the sword and shield, it's nighttime and another song plays.
- Yeah, I also have to agree with the Phantom Ganon music from WW, I like how they remixed music from all previous Ganon battles in there (LoZ (when you enter the room), aLttP, OoT), I think it's better than the actual Gnaon battle music