If you are a system administrator, you should dread any time you use the normal “ls” command and receive a strange error in return. That is a sure sign that your machine has been hacked and ls has been replaced by an unknown program. Gnist blog has a nicely written step-by-step list of what you can do to track back an intruder.
In his case it sounds like the original owner of the machine may have used a weak root password on his machine, allowing for someone to crack it and break into the box. People, don’t forget to use a hard-to-brute force password, and finally disable root login s. Instead, use normal users and sudo.
Finally, if you are doing this in a legal setting and preparing for a possible future court case, don’t forget to make an image of the drive (using dd or Norton Ghost) before your analysis; otherwise the intruder can get your evidence thrown out.
Some other security resources: