I've just moved to a new server and used one of Till's posts to backup all of the data and move it to the new server:
You need to backup /var/vmail, /var/www (or the place where you stored the websites), the ispconfig database, all mysql databases of the websites incl. the "mysql" database, the users and passwords in /etc/passwd and /etc/group. Make sure that you backup the directories with preserved permoissions.
Now, I've done all that but for some reason I keep getting the It Works! Default apache page on all of my client sites. It appears as though /etc/apache2/sites-enabled doesn't have any of my clients in there. Should I also take that from the old server, or should ISPConfig be automatically creating it?