I have a close setup. It just needs a little trick to add subdirectories :

  /*
  !/.emacs
  !/.emacs.d/
  /.emacs.d/*
  !/.emacs.d/themes/
  !/.emacs.d/functions/

You can check my .gitignore here [0].

[0] https://raw.github.com/dgellow/home/master/.gitignore