In the past I've used a little script here: http://forum.joomla.org/viewtopic.php?t=92678 .. to scan my virtual hosts for any exploits that might have been uploaded (eg any PHP Shells, etc).
It's quite a simple but effective script (just searching for keywords and emailing the offending section of code to me to investigate) but it isn't maintained and there's probably better tools out there.
My question is: what tools do other people use/recommend?