What exactly happened? Are you saying the site got defaced or anything more malicious? How many other sites have you got on the server? What kind of access have you got to it (ssh/ftp/etc?)? Do you update the server regularly? There's a zillion questions really
If it's been defaced it's probably a vulnerability in some CGI script that's been exploited by a bot - a service has probably been started to allow access to the server so they can see what's around and upload things. In turn any domains hosted on the server will be used to serve up more 'botkits' which will be used to compromise other webservers.
Hopefully you have all your logs if you wanted to do forensic analysis of what happened - there are various strings you can search for in the webserver logs that indicate a bot intrusion which is probably what happened.
Hopefully they've only managed to gain access as the user the webserver runs as - unless the webserver runs as root in which case... doesn't bear thinking really... well I don't think anyone does that anymore anyway!
For a start I would unplug it from the net if possible - if that's not possible then shut down
all services.
Have a look for any strange looking services that are running. If you're curious you could try and watch any odd service you find (ktrace or lsof or whatever)... double check to see what user they're running at. I wouldn't just go around deleting those things personally, I'd keep them around in 'quarantine' just to look at them more closely and research what impact they might have had.
Check the init/rc scripts to see if anything unusual is set to start on boot, remove those if necessary.
Check the passwd database to see if any unusual users have been added (though to be honest I imagine it's just a CGI attack in which case they wouldn't have had the privs to add new users to the system). Look at 'last' on the commandline to see who last logged in and from where.
Other than that... well I'd probably rebuild my server I think but that's just me. End of day did you keep on top of server updates? Is usually #1 cause of compromise.
Change all important system user passwords. If your web based services include user based systems (well... as with topbetter

) then notify all users if possible and recommend they change their passwords (if they're going to continue using the services... although even so if they use the same passwords on other sites then they could be vulnerable).
I will be happy to help if you want it looking at.