I'm a big fan of Acronis Trueimage.Make sure you rotate through a few backup HDDs to you have a few generations to go back to, or if one of the backups goes bang. If it's a major milestone I snail-mail a set of DVDs to Mum and she files em for me. She lives in a different state so it should cover most disasters of less-than-biblical proportions.
EDIT: Acronis has encryption via a password. I also find the bandwidth of snailmail to be somewhat infinite - 10GB overnight = 115 kb/s, give or take. Never been throttled by Australia Post.