Saw a new problem today: While doing some networking stuff, I accidentally used ports 1040 and 1041 which apparently are known to be used by a trojan. Imagine my surprise when 1) no data came in to my server application and 2) tcpdump revealed that upon every hit on that port, the computer would talk to a different server (most likely reporting the hit.)

So, things I learned: check ports better before using them. Instead of just using wikipedia's list of well known ports, use http://www.speedguide.net/ports.php for a more complete list; and use http://www.speedguide.net/ports.php?filter=risk to find ports with known vulnerabilities / exploits associated with them.