First...wipe the system. Really. You can't trust system binaries anymore. It's like asking your brain to analyze itself. You can't objectively do it. Your system binaries could easily be compromised to hide what is actually going on.
By the time you sort everything out you could easily have rebuilt the thing three times.
Wipe the computer. Restore from backup. (what backup? If you're asking yourself that, you're in deeper trouble...you should probably rebuild the site from scratch and start making a really good backup...OFFLINE backup...plan).
Did you have all updates installed?
You didn't mention your platform/OS/etc. You also didn't mention what your website was (apache? What SQL version? PHP? virtual server, hosted, self-hosted, dedicated server, what kind of hack, how did you know it was hacked, what was in the logs...)
If you're really into trying to secure it, you should probably look at decent backups, checking every day for security updates, and install chkrootkit and rkhunter (if a Linux like platform) and something with a checksum for the files like tripwire.
You can also run audits on your system using Nessus or other vulnerability scanners.
Check your logfiles and audit log files for unusual activity.
Were you able to log in remotely to it? Strong passwords? SSH? Install denyhosts and configure it for locking out unusual attempts to the system.
Check into what method you could use for detecting that you're getting slammed by particular IP's or port scan attempts and firewall them.
Overall...need more info, and you need to wipe the system and reinstall from backups or scratch and get all updates installed. Monitor for file changes. Monitor your logs. Websites really can be run as just a set up and forget thing, but if you're a sysadmin, it takes actual work to run a website "correctly," and it takes maintenance. Even a simple website can be a PITA to keep running and updated.
You can also subscribe to some security lists specializing in your platform of choice (your web server, OS, if you're running SQL or PHP or a specific BBS platform) so you can comb the mailings for vulnerabilities specific to your platform.