Best approach for comprehensive multi-site backup?

I was pretty excited to see that VaultPress now offers multi-site support — and then I wasn’t. As it turns out, VaultPress won’t backup plug-ins or themes from anything other than the main site. This makes it less than useless for me.

So, is there a good, comprehensive, best-practices approach to backing up both files (themes, plugins, etc) and the various live MySQL databases?