I'm glad this post has made it to the top of HN. I've also been looking around at these sorts of solutions over the last couple of weeks. I hadn't rolled anything out yet but s3ql was the leader for me at the moment. I don't know so much about the encryption side but to be honest it's lower down my list of priorities.

Another solution I've seen people using is attic[0] as a centralised backup for multiple machines and then running s3ql to push that over to s3.

[0] https://attic-backup.org