Dunwich building, has a nice creepy feeling to it, especially as you can see how the workers eventually turned into ghouls. Another is Vault X (can't remember #), where you have these purple flashbacks...
Metro stations are a bit scary...
Of course, being level 20, with power armor, and loads of weapons/stimpacks/meds....there's not much out there that can really pose a threat (barring a couple of deathclaws showing up).
I recommend that you play the game at night, with the lights off, the sound turned up...and immerse yourself in the game. Then when something freaky happens, you appreciate it more.