I’ve been using Duplicity (http://duplicity.nongnu.org) for half a year now, and it works wonders. It handles transfer via ftp, ssh/scp, but also various other schemes (Amazon S3 for instance). It also handles GPG encryption of your backups, if privacy is a concern (can do without, though). And the cherry on the cake : It’s easy to set up.

I’d like to add a word about the awesome service rsync.net provides. They are a great disk-space providing company, with very low prices and awesomely competent support. I swear I have no link with that company (other than being a really happy customer).