Mathematica notebooks are, of course, plaintext files -- it seems reasonable to expect that they should play nice with a version-control system (git in my case, although I d
Well, my solution is not using Notebook for tracking, but using plain text files (not the "Notebook" plain text).
Whenever you have a notebook, you can use the "save as..." menu to save the current file as a plain text file. When you need to load it, simply open it with Mahthematica. Tracking this file would be much nicer than tracking a Notebook file. I'm unsure about what features you may lose by using plain text format rather than the Mathematica Notebook, but I haven't found any defects so far.
Reference: http://www.topbug.net/blog/2013/05/02/track-mathematica-source-files-with-version-control-systems/