Rkhunter is an intrustion detection program for Linux OS which has been widely used by many server administrators. Sometimes there is a false alarm but most of the time you need to check the problematic areas Rkhunter points out.
NEW: November 30th 2009 – Rkhunter v.1.3.6. is available and this how-to is updated.
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Michael Boelen, the author of RKHUNTER rootkit checker has made another nice auditing tool – Lynis. It works on many Linux/Debian/MacOS/BSD systems and provides you the admin important information about system configuration and security issues.
Update: On 15th December 2009 there was version 1.2.9 released. I updated this how-toa bit late, but better than never 
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I always want to know when root logs in to my server. It is a security measure I cope with in my mailbox deleting mails after I logged in as well. Here is a little help for you all to receive mail when root logs in via ssh.
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