There is a better solution than starting every virtual host in a seperate instance, which is wasting ressources.
You can set open_basedir dynamically for every virtual host you have, so every PHP script on a virtual host is jailed to its document root.
php_admin_value open_basedir \ "/www-home/example.com/:/usr/lib/php/"
If you set safe_mode on, then the script can only use binaries in given directories (make a special dir only with the binaries your customers may use).
Now no user of a virtual host can read/write/modify the data of another user on your machine.