I'd have to agreed with Valkyrie Profile and Vagrant Story, as well as Shadow Hearts: Covenant. Threads of Fate was good, and even though the actual game was pretty crappy, Legend of Mana was a pretty decent soundtrack. I also think that Grandia 2 was incredible, and I am of the opinion that Final Fantasy Mystic Quest has one of the catchiest RPG soundtracks ever. Need to mention Legend of Dragoon too, I guess.
The Xenosaga series is by no means underrated musically, but there aren't enough remixes. The first episode's battle theme is my favorite of all time.