You don't need sophisticated planning to play a prank on someone. If executed properly, even the simplest prank idea can help you to pull off an amazing prank on people. Scribbling something on a piece of a paper and sticking it on someone's back for instance; simple, but effective. Here are some tried-and-tested effective practical jokes.
It will take some time for the cheese to rot, but once it does, the entire room will be filled with weird smell. Your friend will keep wandering where this smell is coming from. Have fun as he launches a massive hunt for its source.
After re-arranging all the keys in the same way, just sit back and enjoy, while your friend pulls his hair off. Just make sure you use this trick on someone who is not well-versed with typing. It won't be effective when tried on a person who types without looking at the keyboard.
Soaping the Car
You can use a bar of soap to draw or write something on your neighbors car. It is time-consuming and frustrating to wash it off the car. You can slip into your neighbors porch and scribble your 'heartfelt' messages or draw smileys on the car windshield.
Next morning when your neighbor sits into the car and checks the windshield he will be in for a big surprise. You can sit back and enjoy his reactions, while you see him try his best to wash off your artwork.
Going a step further, if you find the door of the car open, sneak into the car and soap it (write on the windshield) from inside. When your neighbor sees it, he will try his best to wash it off from outside, only to realize that it is written from inside.
Something like "This is the FBI. All calls being made to this number are being traced and recorded." will work wonders. Don't forget to set the answering machine to answer on the very first ring. Your friend will wonder why no one is staying in touch with him. The look on his face will be worth seeing when he realizes why exactly people are staying away.
Similarly, you can set a weird message on your own answering machine and see how each caller reacts on hearing this message. Make sure you call them after they hang up. You don't want people to misunderstand.