Best story I remember there was this arrogant guy that worked with on the Unix department. He was into FreeBSD by that time and had an attitude towards the Linux guys. One day he left his table and forgot his machine open with a root prompt. They took the chance and modified inetd.conf to map a certain port to the shutdown program. People had so much fun shutting down his computer remotely and watching his reaction.
There was also this time working for a smaller company and we would prank each other all the time. I had admin access to the Linux router so I've created a NAT rule to redirect this guy's traffic to a transparent squid proxy running a perl script that relied on imagemagik to turn the images upside down. Got the script from a Slashdot post. Poor guy even tried to reinstall the OS to no avail. He eventually found out and had his revenge by going into my computer CMOS and setting disk access to PIO instead of DMA.
I also remember scaring people through Windows' net send commands and that one where you take a screenshot of the desktop then you remove all the icons and interface bars and set the screenshot as background image. Also randomly adding 'alias ls=exit' to some server /etc/profile.