Appropriately set the directory hierarchy (Fig 8.4, pg286) and permission of the server so that they are owned by a special user and group, e.g., www.
See an example of permission setting at http://thaicert.nectec.or.th/paper/unix_linux/apache_chklist.php#23
Also at times double-check to verify that noone has ever changed your setting or inserted a Trojan horse into the server directories.