For the paranoid:
Clamav for viruses.
chkrootkit for rootkits.
lynsis for the rest - it will also give you hints on vulnerabilities potential security holes.
All can be set up as cron jobs, reporting by mail with variable verbosity to an interested sysop...
I've been running Linux since 1993 ( initially the "Soft Landing System" installed from floppies!) and not had a successful infection take hold yet - however, there are some nasties out there that will trap the unwary so you still have to take the usual precautions: don't click on silly links, sandbox your exposed services, don't run as root, don't install unknown programs, keep reasonably up to date, etc...