Hope it was not posted earlier, but let me get a shot.
After the player kills the last monster, a slightly modified message appears:
You feel relatively safe ... for now.
After clearing a level. 30-90 seconds game-time pass, when Arch-Vile(s) comes up the stairs (i.e. is generated close to them) and starts reviving corpses.
The arrival time and perhaps the number of Viles (1 on ITYTD and HNTR, 1-2 HMP, 2-3 UV and N! ?) should be subject to the difficulty level (the higher level, the sooner Vile(s) arrive). Also, this should not happen too early before Viles can normally appear (3 floors before, perhaps?), and never on special levels.
The arriving Viles don't provide XP (to prevent farming).
This will notify the player to get the hell out of the level, leaving scattered powerups behind.
And perhaps, to give a warning, another message pops up when the Viles arrive, perhaps along the lines:
You feel a great evil coming!
All in all, I think that this will really add to the horror feeling, and I beleive it would not be difficult to code either.
EDIT: Of course, the player should _not_ be aware of this level event before he clears the level, in any way.