One 'prank' that came perilously close to 'dude, not funny' was on the old Forgecraft series. You know those cicadas from Twilight Forest? They filled DW20's whole base with them. Hid them behind walls, under machines... everywhere. It took him like three or four episodes to get rid of 'em all.
One that I did was pretty cute... guy had his AE system set up. I... installed a player detector hooked up to a redstone latch that turned off his security terminal, meaning he was no longer authorized to access it. However, the player detector only went off when he was directly adjacent to the ME Crafting Terminal he'd installed in his main crafting room, and at no other time. The even better part is that if he accessed it from an extra block out, it worked just fine. His wireless access worked just fine, unless he was directly adjacent to it. So to him, it seemed like an intermittent bug with his security system. It took him a couple of days of on and off tinkering before he finally broke down and asked me for help.
He was one of those guys who did wiring by rote rather than understanding the system. But I got him to swear off the destructive/theft type 'pranks' he thought were funny in exchange for fixing it.