I think the scariest (or at least, the most atmospheric) video games don't use music at all, save for special instances like boss battles...it builds up the suspense, so when music does play, you notice it, and you know something special is coming...and, if you're like me, you start worrying about what it might be. Dark Souls did this quite effectively in my opinion, keeping you in utter silence most of the time, then ramping it up to eleven with ominous and/or pulse-pounding boss battle themes.
That said, one of the most disturbing game levels/music combination that I can think of is the section of Metal Gear Solid just before you fight Psycho Mantis. It's a quiet, mostly deserted area, noticeably more ornamental than the rest of the base, and there is that haunting, eerie melody playing in the background, occasionally building to a vocal climax before getting a lot lower in pitch...it had me jumping at shadows the first time around.
Final Fantasy VIII has some good eerie moments, as well. A Sacrifice and Succession of Witches are both very creepy themes, with the Ominous Latin Chanting and messed-up visual distortions and general acid-trip-possession thing Edea has going for her.