If you are running an Apache server and are getting hit by httpd floods that overload your server, installing Nginx in front of it (nginxcp.com is an easy to use module for Cpanel) may be the option. Then you need to ensure the following modules are loaded:
FastCGI --> http://wiki.nginx.org/HttpFcgiModule
Limit Zone --> http://wiki.nginx.org/HttpLimitZoneModule
Limit Conn --> http://wiki.nginx.org/HttpLimitConnModule
A great source for some of this can be found here: http://www.cyberciti.biz/tips/linux-...-security.html