sudo apt-get install rkhunter chkrootkit logcheck monit
rkhunter and chkrootkit will both look for insecure configuration, permissions, and known root kits. rkhunter will also maintain a database of the signatures of your system binaries. I assume there are overlaps between the two. I don't really care, I run both.
logcheck will watch your logs and email you when something shows up in a log that doesn't match a configurable set of regular expressions. When I add a new piece of software to a system, logcheck goes berserk. I go through the emails I receive and add in new regex's to ignore the harmless notifications until they finally taper out and disappear, only leaving me with the true exceptions.
Look over the documentation for all three of these, and make sure that they're actually running. Personally, I don't want an email unless something is wrong. If I get an email every day, I'll start to ignore it. I don't think I'd notice if an email I was ignoring didn't show up, so I optimize for no output unless it's something I should read. I chase down the cause of every exception in my logs. No excuses. If it isn't an exception, I add a regex to logcheck.
I run monit because it is pretty easy to set up, and it sends me an email when a server process gets changed or restarted. It lets me enforce limits on a server process, so I can potentially get warning of an attack as it happening. I suspect monit is nowhere near the most sophisticated tool for this purpose, but it meets my needs very well.
As for other basic security stuff... Don't use port 22 for ssh, use something much higher so that you won't get the continuous pounding on the front door that an ssh server on port 22 receives. Disable root login, as well as password login. Use certificates to log in to your machine. Configure servers to listen to 127.0.0.1 whenever you can. Install a software firewall to only allow access to http and ssh anyway.
Unless you've done something stupid with your web app, you've made it incredibly difficult to impossible for script kiddies. If you piss off an elite black-hat, it's probably safe to assume they can own you, and you likely won't know it. So make good backups, with regular offline backups that can't get destroyed by a hacker with a particularly malicious bent.