I really like Markdown for its simplicity and the fact that it allow to write text-based documents with very few requirements: You just need a text editor (mine is Emacs but this doesn't really matter).
Long ago, I wrote a little post entitled Markdown everywhere, when I started evolving from old typesetting habits ($\LaTeX$ or Context) to more simplified markup languages (before Markdown, I used to use Asciidoc). For more elaborated ideas on combining $\TeX$ and Markdown, please see How I stopped worrying and started using Markdown like $\TeX$. I still like $\TeX$-based documents, because it offers so much flexibility and great rendering options; here is an example with a custom Context template. Now, it is clear that Markdown gained enough popularity to come in various flavors as the main texting tools in several software, e.g., the R statistical software.
There are a number of great review of available software to edit and process Markdown files. For example, here are two recent articles I found with little Googling:
But see What is Markdown? to learn more about.
Recently, I heard about Deckset, which looks like a really great tool to publish nice looking slides using Markdown only. Unfortunately it appears that is is only available for OS X 10.9, while I choose to stay at 10.7 (long ago again). I know how easy it is to produce Beamer slides with Pandoc and Markdown, the advantage being that we are not restricted to HTML+JS output.
Hopefully, this is not the only solution and there are a couple of links about standalone apps or wrappers.
Landslide: a Python-based slideshow system, which Chris Fonnesbeck was using for one of his course:
I'm pretty sure I bookmarked other links from Twitter, but well, that's where Twitter sucks: it's hard to find something you posted or bookmarked, say, three or four months ago. Here is all what I found by looking in my recent tweets:
By the way, Pandoc can also make use of Reveal.js. Of course, if you are using R as often as I do you may well know that RStudio now has a nice Presentation mode. That's what I used in my latest course, although I would have preferred to use Slidify (when I started writing this course, I wanted to publish everything on Rpubs and RStudio was great for that).