Take a look at "Corpse Party." It's a horror themed, visual novel for the PSP which uses 2d orthographical game play.

Some thoughts on how it succeeded with being creepy/scary:   
   - Had an inspection system (as mentioned before) that gave either a description or picture (many possibilities with this, one of the pictures would have a popup after a couple of secs)
   - Pixel art of gore/blood (simple, but effective)
   - Had animated scenes outside of game play to enforce plot (you can use this to make up for the pixel art)
   - Sounds, Corpse Party had the luxury of having the scenes voice acted, but simple sounds like a door creak or a scream should be effective
   - Setting, a dark abandoned elementary school with dead children/people is much more creepy than the standard dungeon that looks like crypts from diablo
   - PLOT, I think this is the most important point. Read horror books if you have to. A good plot will make ANYTHING creepy.

Just some ideas to help you out. As for general creepy things/monsters try: ghosts of children, beheaded/mutilated people, people being "smashed" into walls/floor, and you get the idea: blood/gore