"Light from the Netherworld," the background music to the opening movie. Incredibly eerie and chill-inducing. Even if you've never even seen the opening movie, you can tell just by listening to it that something inexplicable and unearthly is going on. And now the Orchestral version is out, edited into the Opening FMV.
"One Who Bares Fangs at God" can ONLY be heard during the Anti-Climax Boss fight with Urobolus/Miang even though it's one of the best songs in the game. Which serves to redouble on the final battle's subversive principle — both the battle and the accompanying music are anything but the standard Final Boss fare, for dramatic purpose.
"Grahf, Emperor of Darkness". When this comes on, it's obvious that either a boss is about to get a powerup or you are about to have your ass kicked.