Run chkrootkit and rkhunter and maybe even Nobody Check from WebHostGear.
To prevent this from happening in the future: harden your server! Secure your websever, your PHP, your tmpfs partitions, etc.
It's possible that your server has been compromised by script kiddies, you could always ask a company like
www.seeksadmin.com to perform a security check and to secure/harden your server.
I suggest installing Snort with ACID which might help you detecting DDoS attacks in the future.