A 4th option that is comparable to git-fat is git-bin (https://github.com/seeq12/git-bin/tree/v1.5). We at Seeq use it to store large binary files that would otherwise clutter the repo, much as you describe. While git-bin is a C# project, it runs well under Mono, and we use in on Windows, OSX, and Ubuntu. It's a small, simple, program that fits seamlessly into the standard Git workflow. We forked it from the original author and have been actively updating it to increase its robustness and ease of use.