Internal System Backups
As many of us probably have two hard drives on each server, to act as a backup drive, I personally would like to see an internal backup option.
This would probably be easiest to implement with rsync in conjunction with mysqldump, and it would be best to have the base configuration in ISPConfig itself.
Specifically, under 'Tools' would be a section to specify the partition being used for backup, and perhaps a subdirectory. ISPConfig would then create a database backup directory, and a site backup directory. Cron jobs can already be scheduled for each site, so it shouldn't be hard to have the main sysadmin able to do the same thing for the machine - thus backing up the /var/www/* directory (with symlinks), the various critical configuration files from /etc/, and dump the databases. Since this would be done _internally_, it wouldn't get hit by the php memory limitations that people with large databases run into with phpmyadmin.
In fact, if the databases are dumped individually (since ISPConfig knows of all the databases), then the client could be offered a straightforward download link that connects to the latest backup of _their_ database done by the system.