Git IS a key/value store database. (A filesystem is a kind of database, too, of course.) There's a good summary of the internal data structures here -- http://www.kernel.org/pub/software/scm/git/docs/user-manual....

As I've said elsewhere in this thread, tracking metadata (path and sha1 hash) for large binary files in git and otherwise ignoring them via .gitignore works quite well. I'm pretty sure the "right tool" is either rysnc or something similar.