IMHO, pranks are an integral part of crew unity and job sanity in this business. For those of you who never flew prior to 9/11 I'm truly sorry, because it was such a different environment then, and much more light hearted.
A good FA knows that everything is in good humor. A great FA will figure out ways to get back at the flightdeck with a good prank of their own. (Just remember if you dish it out, you'd better be able to take it too!)
As for some of the pranks I've seen/done/or heard about:
In the CRJ, turn off the window heat in cruise on one side of the cockpit, then call the flight attendant up. Tell her that you think that you have exceeded the speed of heat and have her feel the cockpit windows (one will be warm, the other cold). Then instruct her to go back and check the cabin windows and report back on the temperature of each.
Explain that you feel that there is an air leak in the aircraft. Tell the FA that you know all the doors are secure (show them the door synoptic page), so the only thing you can think is that air is leaking out the lav. Tell them to go back to the lav and sit, forming a good seal, and then listen for any air leaks/flow. Report back to the cockpit with the results.
Lots of potential with barf jokes. Nuff said. Just make sure you don't have a sympathetic puker in the crew.
Rubber dog poop can be fun too.
Here was a good one pulled on me by another crew- Sitting at the gate, getting ready to depart when another aircraft (CRJ) pulls up beside us. The CA asks over the company ops freq if "we're up." I reply yes and he asks me to watch his passengers deplane. (I assume that he's running an engine or something and wants to make sure they don't wander around). I say okay, then keep and eye on them. Every one of them steps of the plane and smiles and waves. Not wanting to be a jerk (but also trying to get the paperwork done for my flight), I have to stop and wave back and smile. Finally everybody is off and the captain of the other flight comes over to us. I ask what was going on... his reply: "Oh. I had a really bad landing, so to take the focus off of me, I told them that it was your 21st birthday and they should all wave and wish you a happy birthday as they deplaned."