My 'little' off-site Raspberry Pi backup/remote storage project will probably use a combination of Bittorrent Sync and rsync. The latter will be used to backup personal information, but I want that data to be absolutely secure. So I want to use encryption. Preferably by using container that I can mount (e.g. Truecrypt or the Apple OSX encrypted disk images).

The problem with containers is that many backup solutions tend to backup / transfer the entire container when a change occurred. Thankfully, rsync only copies the changes.