Apart from the Final Fantasy series, which is undoubtedly my favourite, I think most JRPG fans will agree that Resonance of Fate has a memorable soundtrack. The tracks that particularly come to mind are:
Xenogears - The game's story alternated between compelling and a complete mess, but the music made that game for me.
Xenoblade - Better story, though I've had my fill of Gnosticism to last a lifetime. When the game wore out its welcome, the music kept me in it. Some of the nighttime themes are among my favorite game compositions.
Chrono Cross - The whole damn game.
Some notable tracks off the top of my head - Somnus, Apocalypse Noctis, Rose of May, Home Sweet Home, Cosmo Canyon, Beware the Forest's Mushrooms...