VaultPress, Automattic’s WordPress backup utility, just announced support for Multisite.
VaultPress support, also known as VaultPress Safekeepers, are available between 8am-5pm PST, according to their support page.
One thing that is noted in the help section for Multisite is that each site will require its own subscription and registration key. This could be cumbersome for a network owner and become cost prohibitive. I hope they reverse this to allow you to backup an entire network for one price.
VaultPress is said to be the benchmark for WordPress automated backups, but there are strong competitors out there, like BackupBuddy by iThemes.
One of the main differentiators between VaultPress and other solutions is that VaultPress is a hosted solution. Backups are made to an Automattic-owned server. BackupBuddy, for example, can backup to any FTP, Amazon S3 account, or e-mail, easily — which is cheaper in the long run. So it really depends on what you’re looking for in a backup solution.