Plus one on the Secret of Mana love train. I was actually looking at videos of various groups performing the kecak dance recently on youtube, when one commenter pointed out the Dark Lich boss theme had the main part of the chant in it. I thought that was really neat.

Anyway, some good ones that I can think of off the bat:
EarthBound
Pocky & Rocky
Kirby Super Star
Grandia 2
Shadow Of The Colossus
Silent Hill
Fragile Dreams