Eric Lamb at Mithra62 just released a major update (version 2) to Backup Pro, which is an advanced backup add-on for ExpressionEngine. It makes it simple to regularly backup both your ExpressionEngine site files and database.
The backups can live right on your server but for even better protection, Backup Pro 2 uploads your backup to either Amazon s3, Rackspace Cloud, Google Cloud Storage, or any remote server via FTP. Even better, Backup Pro 2 allows you to use up to three remote locations at once, so you get redundancy and safety for your website data.
I personally use Backup Pro to handle extra backups for my important EE sites. I encourage you to check it out.