bedup implements incremental offline whole-file deduplication for Btrfs.
It works on mainline kernels (Linux 3.3 is required by the file locking implementation, 3.6 is required for cross-subvolume operation), using the clone ioctl (which exposes Btrfs' copy-on-write functionality).
Probably, the package with it could include a script for cron to run deduplication regulalrly, say, every day (or week) at night -- which could be turned on by those who wish.
[slava@dubrhome ~]$ apt-cache search bedup
i586-bedup - Deduplication for Btrfs
bedup - Deduplication for Btrfs
[slava@dubrhome ~]$ apt-cache show bedup
Section: File tools
Installed Size: 478992
Maintainer: Vitaly Lipatov <email@example.com>