In my opinion, "a bunch of Markdown files" is good because:
It's easily viewable in GitHub
It can be made into a Jekyll (GitHub pages) site easily
It can be made into a Sphinx site easily
It's a common documentation format that you can get some tools to generate to
You have just read Use Markdown for documentation, written on February 19, 2015. This is Today I Learned, a collection of random tidbits I've learned through my day-to-day web development work. I'm Rico Sta. Cruz, @rstacruz on GitHub (and Twitter!).