It depends on what you are looking for. You could set up Nessus (or nmap or something similar) to run active scans. Nessus has a (free) home feed, as well as a scheduling option. Another front end for it would be Seccubus (
http://seccubus.com/).
Something lighter would be tiger, which emails you differences/changes From the Debian description,
"Debian's TIGER incorporates new checks primarily oriented towards
Debian distribution including: md5sums checks of installed files,
location of files not belonging to packages, check of security
advisories and analysis of local listening processes."
You might also check out chkrootkit and rkhunter.