Ok, here is a list of a few programs I’d advise anyone to use who is running a server on the internet (or thinking of doing so).

• aide or tripwire (they can check and report if files on your system get changed, configurable levels). If you use tripwire, don’t forget a “tripwire –check -I” after you do any updates.
• logcheck will check your system logs, and report anything out of the ordinary (“ordinary” is defined by a list of ‘normal’ rules, and anything you add)
• tiger goes farther than logcheck, it actively checks your system and reports anything strange (files not belonging to packages, users or groups that got added, …)
• grsecurity adds more security features to your kernel (at least use the basic features and the possibility to turn off module loading after boot)
• rkhunter, chkrootkit scan the system for signs of rootkits or other malware. just install, make sure they are executed daily by cron, possibly tweak rkhunters config a bit (I had problems with unhide and current kernel versions)

I’m not saying that setting up and tweaking all this software and actually reading the emails they generate will make your server super-duper secure, but they will reduce the risk of running a server open to the internet and alarm you if somthing strange is happening. It is important to read and understand what theese programs mail you. Yes, you will get false positives from time to time. And yes, you will have to adjust the config now and then due to package updates; but I get about 3-4 mails a week, and that is definatly ok considering the amount of data that gets checked.