Seconded for SH, especially Wounded Warsong and Breeze in Monochrome Night.

The BGM for Baaj Temple in FFX is wonderfully atmospheric and dark, perfect for the Aeon it hides. It sounds like a lost level of Legacy of Kain: Soul Reaver.

Speaking of which the main theme of LOK:SR (Ozar Midrashim) is wonderfully creepy.