If you don't want something quite as flashy/expensive as R1Soft and you're using cPanel/WHM then you can consider 'CPremote'. It uses rsync to backup all the accounts on the server and stores it in a format where you can just take the backup data for 1 account and restore that entire account (files, databases, emails, dns etc.) from the data. As it uses rsync, it only copies data that has been changed. It puts very little strain on the server at all as it does not compress the data like normal cPanel backups. I have been trying the software for a little while now and the support is great, the product is reliable and it all works as it should.
The downside in comparison to R1Soft is that it really is for backing up the data on the server (i.e. on a daily/weekly/monthly basis) and not for providing your customers with a way of backing up their data and easily restoring parts of it as they need it.