here are som tips to protect from hacker's
read the error log file apache generate and find the php scripts they use to access the server and secure them, like Gallery and Yabb ..
chmod 700 all programs used to compile source code and lynx, wget links whatever they can use to download stuff.
Use open_basedir as whm provides, its not for fun they put it there ... This limits the access to where they can go
add the noexec option for /tmp dir in /etc/fstab
Disable all php functions who gives shell access and simular.
Use a firewall to close all unused ports and close outgoing trafick where not needed so they can not use the server as scanner or for DOS.
Cpanel! It would be great to see a iptables script inside WHM - how much work can it be and how much will it help?
Also it would be good to have a script that can be used to test websites for unsecure php.