There isn't an easy and automated way to do this from a monitoring environment. Perhaps the best method is regular Nmap or Nessus scans of your hosts (though this has some risks and you will have to ensure that you set up both to scan in a non-intrusive manner) with the output compared a pre-defined baseline. Both tools will also generate a lot of network 'chatter' and if you have an IDS/IPS installed, then this will potentially look like an attack and generate false positives.
In the event your host may have been compromised there is also hardscan, a netstat replacement for scanning local ports, attempting a handshake and outputting the results. This can often help in identifying a host infected with a rootkit that has compromised ports open.
This was first published in June 2007