Although git-annex is not a backup system, it works for me as one to backup photos, disk images, some documents etc (although I use it with hubiC and self-hoste

Although git-annex is not a backup system, it works for me as one to backup photos, disk images, some documents etc (although I use it with hubiC and self-hosted SFTP storages, not S3). Maybe it could meet your requirements, too. Files (or chunks, if it's enabled) are gpg-encrypted (to a key or using a symmetric passphrase) and could be stored in nearly anything that could store named blobs. Supports various modes (archival, backup, RAID-like). Performance is fair for me. Downside is that it's not a "real" filesystem, but a git repo that tracks metadata, plus blob storage. Assistant daemon saves a lot of keystrokes, though. There is also some FUSE-based implementation, but I haven't tried it. Getting started is easy, so I suggest taking a look and toying around for half an hour. Another downside is that it - being a git repo - may have problems with storing another repositories inside. Haven't tried this, though.