have you seen: https://github.com/apenwarr/bup
"file backup system based on the git packfile format. Capable of doing fast incremental backups of virtual machine images. "
Sure, git-annex can use bup as a special remote. This way you get bup's nice properties of storing big stuff in git with binary deltas, with git-annex's nice properties of a normal-looking file in a git clone.
