If you are running a Unix/Linux/BSD dedicated server, I would suggest installing and running tripwire. It is a nice file integrity checker. You should probably run it about once per day to make sure no one has been messing with your system.

Since the security problems that my organization had two weeks ago, we have been running it several times a day.

You can find TripWire at http://www.tripwire.org/.

Best regards,
Frank Rietta