Re: [DF] "Sinkhole of Evil"
 

The Hellmouth from the TV show Buffy the Vampire Slayer could also be an inspiration.
> A gate to an hell dimension and of course a seal to be protected/broken/... deep in a dungeon
> Dark prophecies about the place
> It would be the place of choice to conduct dark rituals

If using RPM, any quirks on a spell cast there should have an evil taint.
Same with all magical critical failures.

If using powerstone, fully draining one and allowing it to recharge fully within the Sinkhole could give it a evil-themed quirk.

A penalty to self-control rolls could be in order too.

Re: [DF] "Sinkhole of Evil"
 

The Hellmouth was both a Font of Evil and a Weirdness Magnet. I haven't seen the idea of locations that are Weirdness Magnets in-game, but it seems to fit the setting, and probably a few others. Depending on the Dungeon (good idea, Anthony) and the GM, it may be that the genius loci is a Weirdness Magnet as well as a Font or Sinkhole of Evil, or that the location is, or it may be that this particular Dungeon is only one or the other.

Could also be the way that living Weirdness Magnets and beings with similar disadvantages (Demon Magnet? Evil Sanctity Enhancer?) are handled in-setting: choosing or compelled to take up residence somewhere away from civilization, where the problems and strangeness that they bring cannot trouble their neighbors.

EDIT: Now I feel kind of tempted to design a dungeon on this theme. If I do, don't expect it to happen fast.

Also, I think Paranormal Waste Repository may be somewhat relevant to this discussion.