If I want to print a markdown file from GitHub as it appears on screen, for example:
https://github.com/RestKit/RestKit/blob/master/Docs/Object%20Mapping.md
If you have an Instapaper account, navigate to the README.md file, save the link to Instapaper, then open the "text" option in Instapaper on that link. Most of the "clutter" is removed and the page prints well.