php|architect has a link to a handy little utility to help you protect your server against malicious PHP, HTML, CGI and text files - PHP AntiVirus.

GPL PHP AntiVirus for webmasters. Scans your web server's file system for dangerous and malicious code in public HTML, PHP, CGI and text files, usually caused by defacement or security holes in shared hosting accounts.

Point release now available with minor feature improvements. I have modularised the configuration file, and added default options if the file cannot be found.Support has also been added for scanning plain text files, more script/HTML files, flat data files and CGI scripts.

164 new virus definitions have been added to the database.

Running something like this isn't going to be the ultimate in protection for your server, but it can give you a bit more peace of mind...