I store my configuration files as a git repository. This gives me the following important features:

• I can easily setup configuration on a new machine, simply by cloning the repository.
• I can have different branches (currently I am using them for different operating systems).
• I can easily rollback any changes (even though I edit my configuration files in vim and I have persistent undo enabled).

Requirements

To implement what is described here, you obviously will need git. I suppose that you have some remote place to store the repository (I am using my own remote server and gitolite but I suppose that anything – for example, GitHub – will work as well). Also using a shell which allows to set up aliases makes things more convenient. I am using GNU Bash and PowerShell and both of them work.