After finding Backupsy (and RamNode, which a commenter suggested), I've found the holy grail of backup solutions. I will write a simple backup script that mounts a remote directory (through SSH or whatever), mounts an EncFS directory on that and rdiff-backups files onto it. This will give you encrypted, snapshotted backups using open-source systems, that are better than Duplicity because you don't have to be creating…
What I am looking for is a folder that syncs, but is secure and open source.
BitTorrent Sync is the closest to how it should work, but is not open source: http://labs.bittorrent.com/experiments/sync.html