This is one way to pass some data (API tokens, etc.) to your Jekyll templates without putting it in your _config.yml file (which is likely to be committed in your GitHub repository).
Copy the environment_variables.rb plugin to your _plugins folder, and add any environment variable you wish to have available on the site.config object.
In a Liquid template, that information will be available through the site object. For example, _layouts/default.html could contain: