Disclaimer: I do not actually intend to carry out any of the proposed pranks that may be mentioned in this thread. I'm actually just collecting ideas for writing purposes.
That said, here's the best prank I've ever heard of:
So, you take a raw hot dog, thaw it out, and put it in your pocket. Best if you have somewhat baggy pants. You head into work/school/wherever you need to be that day. You approach your victim with your arms full, acting like you're in a rush. You tell them you need to get something (keys, wallet, etc.) out of your pocket, and you don't have time to stop- and you ask them to reach in and grab it real quick. Obviously, the set-up is more believable if you're not standing right next to a desk or something that you could just put your pile of *whatever* down on. Anyway, they reach in, feel the hot dog, and immediately freak out.
For bonus points, have someone video tape it.
Here's one more that I've actually fallen for. It's just so ridiculous, it doesn't even register that it might be a joke until it's too late, lol. So for this one, it's best if you have a couple of friends in on it too- makes it much more confusing for the recipient. You have a get-together with a couple friends at your house or something, and you explain the prank to all but one friend before they get there. You get a cooler, put some ice in it, and fill it with bottles of water, or gatorade, soda, whatever it is you happen to have a lot of- but you put them all in upside-down. Your friends arrive, and you start gaming, watching TV, or whatever it is you were planning to do... nothing seems out of place. Eventually, either your designated victim asks for a drink, or you offer him one (it's best when they ask first, but don't wait too long before you offer, or it'll seem like a set-up). So you tell him/her that there's drinks in that cooler over there, and say something like "oh, but we only got the upside-down kind". At this point one of your other friends should chime in and say something like "yeah, be careful when you open it, it might spill". Try not to laugh, smile, or act suspicious, like staring at the victim to see what he does. But, when executed properly, they should pull the bottle/can out, holding it up-side down the whole time- as if it's supposed to be that way- and they will usually hesitate before opening it. I know I did.
I've even seen one person actually open the bottle while holding it up-side down.