Hi Aldert,
I use Samhain and AIDE on my little system. They do similar things, basically looking for any filesystem changes and emailing you if they find a problem. Samhain runs as a daemon and emails you instantly. AIDE runs as a cronjob as frequently as you like.
One minor issues is that Samhain issues a lot of emails (in the 100+ range) on reboot. All of those emails were going through spamassassin on my system which then really loads the system down. I fixed it by having spamassassin skip local messages sent to me.
I'm not an expert on any of these -- just set them up via the debian documentation.
Best wishes,
Vinod