Here is my older paper on discovering compromise systems, I just wanted to highlight it for my newer blog readers:
From "Issues Discovering Compromised Machines" by Anton Chuvakin - "One of the latest security books I read had a fascinating example in the preface. The authors, well-known and trustworthy experts in the field of security, made an outrageous [is it, really?] claim that most of the Fortune 2000 companies have already been penetrated by hackers (and have been in that state for years!). Hackers move in and out at will through the backdoors and other covert channels without the security personnel knowing or even suspecting it. Without being able to verify the validity of this, I decided to look at the problem of reliably discovering the compromised machines on corporate networks..." Read on.