Lynis is a nice little application that checks a linux (or possibly other UNIX-type operating systems) for standard misconfigurations and possible security threats.  Unlike system integrity verifiers, like tripwire or aide, Lynix doesn't monitor file changes, rather system configurations and installed software for possible security threats.

It generates reports for review and includes a cron option that optimizes output for automated scanning (removes text color, uses certain switches automatically to decrease line lengths, prints only the warnings).  You could even write a script to cron that emails you the results every time it runs so you can be kept up to date on its findings with minimal effort.

Lynis is still under development and it really doesn't do a great deal at the moment, but it does have plugin features so you can expand on its functionality.  I'm sure with time, this software will evolve into something really useful.  Don't be scared to contribute to this, if you're a system administrator or penetration tester, get in there and write some plugins or contribute code upstream.