First, many thanks to the author for a reasoned and researched post. The editing/mass-adoption sides of the text formatting story vis-a-vis markdown were well told. I think the story of text is important and misunderstood and evaluation brings better understanding. So please take the rest of this as a supplement more than an argument, even if a lot of it is a disagreement about the value and future of markdown and wh…
I have over 3,000+ posts for my blog [1] and I can answer that: HTML. All my posts are stored in HTML [2]. A few years ago I started using my own markup language (a mashup of Markdown and Org Mode) but I never store anything in that format; I only store the rendered HTML output. That way, I don't get stuck with a markup style that I no longer like.
Also, I don't see Microsoft Word going away anytime soon. Every other developer at $JOB writes documentation in Microsoft Word [3]. On a corporate managed Windows laptop. Joy.
[1] http://boston.conman.org/ I've been blogging since December 1999.
[2] Each post as a file. The storage format has not changed at all in 22 years.
[3] I inadverently found myself working for an enterprise company when the company I was hired at got bought out.