Change one or more of the shortcuts on your victim's desktop to point to a funny audio file (suggestions: search the internet for "Banana Phone" or "Peanut Butter Jelly Time").
Right is Wrong
Change his mouse to left handed configuration (assuming he's right handed, reverse if left handed).
Sounds Like Trouble
This prank is perfect if you have a desk right next to a co-worker, and you both have similar speakers. Just swap the position of your speakers (but leave them plugged in as normal). Then occasionally cause weird sounds to come out of your speakers (on his desk) at random times throughout the day.
Unplug the keyboard and/or mouse from the PC.
They're Gonna Die
Do an image search online for "blue screen of death" and set that image as the screen saver on the victim's computer. That'll give them a real scare!
You've Got Mail
Change the victim's e-mail alert sound to something annoying and turn the volume up really loud on your victim's computer. Then send them an e-mail.
Start 'Em Up
Change the "start up" sound on your victim's computer to something funny or embarrassing. Make sure the volume is turned up all the way when he or she arrives to work.
Has your victim been working on an important document on their computer? Carefully hide the document in a safe place, then create a fake document with the same name. Fill the document with gobbledy-gook or a funny story. At the bottom put "April Fool's!"