Well, this is a pretty cliché list as far as creepy game tunes go, but it doesn't make them any less creepy!
And here's something really creepy. I listed Lavender Town from Pokemon Blue/Red/Yellow above. Well, the remakes, Leaf Green/Fire Red, version of Lavender Town isn't nearly as creepy.
Reverse it, and you get this terrifying piece of music:
The original sounds like everything and everyone is being destroyed before you, and there is nothing you can do. Reversed it sounds like you are searching through the debris and rubble for your loved ones, but they are all gone, and you leave.