If they have a decent size CD/record/DVD/video collection take all the cds etc out and put them all back in the wrong cases (works well as little 'extra touch' on top of others).
As a variation on the cress theme, why not arrange the wet areas/cress planting in an amusing pattern. A crude picture or risque limerick perhaps.
Obtain a car (chance to annoy two people at the same time), take it apart, and rebuild it inside the room (of course it has to be the right sort of car, some shells won't fit through the doorway). Or anything else that can be dismantled and reassembled. Remember to use lots of threadlock when reassembling.
Combine a few of the ideas on this thread for maximum effect.
Make sure your own room is always well secured at all times after he comes back.