3 of us snuck up on this girl we found out had been stealing from our dorm rooms and selling the stuff on Ebay and poured blue koolaid powder on her in the shower. She dyed her hair white Marilyn Monroe blonde, so not only did it turn her skin blue, but it got her hair too. (And she stopped ganking stuff from our rooms!)
Call one of those "theme" strippers, like the Sexy Fireman or Naughty Nurse, to visit them "for their birthday". Make sure 1. it's not really their birthday and 2. it's not really their kind of stripper. Clue the performer in ahead of time and he/she might really camp it up.
Get a box of "Bomber Snaps" (a brand name for those little paper packets of gun powder you can toss onto the sidewalk and make a popping noise). After everybody's gone to bed, pick up the toilet seat and put one packet under each of the little 'feet', or just spaced evenly around the bowl, and put the lid down. The next person to sit down gets a surprise! (Works well in conjunction w/ the Exlax brownies idea Melissa posted.) This can also work w/ a motion sensitive alarm on the underside of the seat, esp. if you need to train somebody to put the seat down.
In the toe of a work boot or old shoe, carefully hide a jelly or cream filled doughnut. Make sure the shoe will be worn that day, and watch the owner find it... with his foot. (Darn, now I want Timmy's.)
Make "apology" or "birthday" chocolate chip cookies. Substitute the white sugar for salt and unsweetened baking chocolate for the chocolate chips. This also works with brownies (and for roommates that won't stop taking your food w/out permission.)
Glue a penny to the bottom of his shoe (best when he walks on a hard floor all day).
When he's not looking, salt his beer.
Mismatch all of his socks, then tie them in knots.
Put a couple of single stitches into his towel while it's hanging on the rack, essentially sewing it onto the bar, just before he goes to shower.