There isn't an easy and automated way to do this from a monitoring environment. Perhaps the best method is regular...
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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.
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