VaultPress is the only backup tool specifically made for WordPress which I would consider using. I don't use it, because last I checked, the costs for multisite installations were too much. It'd cost me a few hundred per month, which is out of my budget for my personal sites.

Instead, I just run a regular old Cron job, which zips everything up and sends it off to Amazon S3 every once in a while. It's much more reliable than a WordPress plugin can be, and doesn't cost any money at all (aside from the obvious hosting costs).