seconding jason, but with not much more to go on, if you have either older, umpatched phpbb or awstats installed on your domains you are vuln to a variety of sql expliots (santy worm, injections, etc). What php scripts are you using? If they are third party, you should probably check out the user forums for those scripts, you will find info about exploits, patching, restoration hints at these boards. If they are home-made scripts, you might want to check out php security forums.
If mod_security is not enabled on your domains, turn it on, should help prevent most future attacks.
Good luck getting everything back in order. I also doubt this was a server-wide issue because if it was, there would be a lot more noise on this board if many users were affected.