This is the obvious winner.
Dark...moody...chromatic. Really captures the urgency of the falling moon in a pretty difficult temple. I can't say enough good things about that song. And around 1:10 you hear this really sexy and subtle melody....just ambient and awesome.
It reminds me a bit of the Forest Temple, only a million times better.
Wind Waker had the most epic overall score. And it had silence at the right times too. Something about the open sea...and the island sounds...
Given the art direction, and gameplay, I'm tempted to say Wind Waker is right behind OoT and MM for most polished and original 3D Zelda title.