I like to use the BackWPup plugin for taking care of backups. I especially like it because it makes backing up to Dropbox really easy. It's available for free in the WordPress plugin at http://wordpress.org/plugins/backwpup/. I've used it for all my personal sites as well as for customers. It makes scheduling backups really easy too.
You'll want to use BackWPup from the Network Admin side of the Dashboard window, instead of on individual blogs. The backup creation screen can be seen in the following screenshot.
BackWPup also comes in a pro version that adds some features such as the ability to use custom API keys for Dropbox and SugarSync, backing up job settings, the system testing wizard, and other features. The free version has been sufficient for most of my needs, but some of the pro features would be nice to have for certain sites. BackWPup is a good backup solution because it will backup your database and will also backup your files.
BackWPup job creation page