I just had a machine upgrade to Debian 6 after a package update - Virtualmin had a bit of a complain when it came to the suexec base directory, and all of the websites on this machine died. When setting the domains to run as mod_php, CGI or the preferred FCGId you'd get:
Failed to save website options : The Suexec command on your system is configured to only run scripts under #/home, but the Virtualmin base directory is /home. CGI and PHP scripts run as domain owners will not be executed.
Looking at their forums they suggest that the issue is a non-virtualmin based installation of Apache - further investigation required but for the meantime:
cd /etc/apache2/suexec nano www-data
In this file remove the top line stating "/var/www" and replace with "/home". Restart apache