Take all his furniture out of his room. Move it somewhere else he would find it like the bathroom, the landing in the stairwell, attic, basement, wherever. Set it up exactly how it looked when it was in the room.
If he's got a dresser, move everything around in it. Take a folded stack of shirts and switch it with a folded stack of shorts. Put the socks where the pants belong. If you want to get really tricky, switch like one shirt with one pair of shorts, but put it in the middle of the pile so he won't notice (obviously do this with several articles of clothing).
If his shoes are organized or on a shoe rack or something, switch one shoe of each pair, but try to get the color to match so its less noticeable.
Take all the button down shirts/hoodies/jackets/anything on a hanger and turn it inside out, then hang it back up.
Take his underwear, put each one in a ziplock bag, add some water, put them in the freezer. Either leave them there or once frozen, put them back in the drawer.