A while back Vanessa posted a script on her site that allows site administrators to automate cPanel backups via cron job:

“This is a simple script derived from the cPanel process that generates full account backups, only in PHP form. This makes the task of backing up your site easier and more reliable by allowing you to generate and maintain your own full site backups.

• Automatic backup via Cron job
• Generates an actual cPanel backup in tar.gz format
• Very easy to set up, and executable with only one simple command
• Email notification when the backup is complete
• FTP option to transfer the backup file to a specified FTP server
• Compatible with monsoon, x, x2, and x3 themes”

You can download the script here:

http://www.v-nessa.net/2007/01/03/cpanel-automated-backup-script/