I’m going to build on Jamie Zawinski’s excellent advice about backups, which you should read first. This is basically that, but with some extra bits. If this seems too complex, then just do what he says.

The plan is to use Backupninja to backup everything to an external USB drive – and also to Amazon S3 or Dropbox, depending on what it is. Backupninja provides a centralized way to configure and schedule many different backup utilities, just by dropping a few simple configuration files into /etc/backup.d/.

I have a multiple hard disk setup for my desktop Linux box - my /home folders live on one disk and / lives on another one. I don’t want to backup everything from the system disk - I can re-install it in 10 mins, and I don’t really want to complicate this …