I store them in a dotfiles repo that gets pushed to Github occasionally. They get symlinked to my home directory, and I use thoughtbot's rcm[0] tool for managing that. Then I just use a small script that I keep updated to handle installation and setup on a fresh computer. I'll need to take a look at gnu stow now. It seems like it'd be a slightly simpler alternative, and would keep my dotfiles folder a bit better organized.

0. https://github.com/thoughtbot/rcm