I found SecoBackup to be a good tool for backing up a Windows machine to S3. They have a 'free community edition' version, but you will still pay more in terms of your S3 costs than what you would normally pay to Amazon. You basically sign up for the SecoBackup service 'powered by AWS' and you pay $0.20 per GB of storage and $0.20 per GB of bandwidth -- so double what you'd pay if you stored it directly on S3. You don't even need to have an Amazon S3 account, they take care of it transparently for you.
I think this is a good tool for backing up certain files on Windows-based desktops. For example I back up my Quicken files from within a Windows XP virtual image that I run inside VMWare workstation on top of my regular Ubuntu Hardy desktop.