I've toyed with Markdown before, but never really understood it or got it. I think now I get it, especially for academics.
It is the Mac Power Users episode that has really brought this home for me. I have personally seen how Microsoft Word files get outdated, especially after I spent some time a few years ago opening and re-saving old Word 5.x files into the newer formats. I do think, however, that there is some security with Word, since Word is so dominant in businesses and academics; there is always safety in numbers, and there is a very good chance that someone somewhere will always offer conversion services, such as Zamzar. Yet this kind of service/conversion is a bit of a pain, might involve cost, and is certainly not guaranteed.
One of the things I have struggled with, and where I think Markdown will be quite helpful, is notes in the classroom. I'm convinced that simple outlines work best for classtime, as they encourage flexibility, a focus on the actual text being studied, and dialogue between students and teacher. They also make for quick re-usage of material in other contexts, classes, and lectures. I have played with various approaches here, from plain text files to OmniOutliner and Evernote. What I need is something simple, yet with some sort of formatting to make scanning the words quick and easy; I need ways to bullet, indent, and title key phrases and elements. So complete plain text is out, as it can't indent and bullet as I would like.
OmniOutliner works great in many ways (I especially like the ability to hide or reveal parent lines, even though I sometimes miss the closed icon and forget text is hiding there), but is too fiddly – I seem to always be messing around with fonts and sizes – and it doesn't have a good sync option (at least not yet, but it's coming soon). The other problem is still the issue of data rot; will OmniOutliner be around and accessible in 5 years? (I hope and expect so.) I've also been disappointed that moving OmniOutliner data to other formats tends to mess up the formatting, so that bulleted indents get wackily thrown off their proper alignments (I've tried various exporting options, but no luck.)
Evernote works quite well for formatting, with some nice abilities to create lists and make text bold. The sync is great in many ways (especially its omnipresence), but it's not quite as lithe as I would like. Because I do use Evernote for archiving lots of different kinds of files, I end up having sync and discovery lags as I look for my lecture notes among my various items. There is still the data rot issue, along with formatting issues. Additionally, one must always wonder about file corruptions with these formats; with plain text, corruption is much less likely.
Using Markdown, as David Sparks says, you have simple, plain text files that can be converted into unsophisticated formatted text – and that's just what I need. So I would have my original text files, which are fairly future-proof, and I can have my peek at those TXT files during classtime with a Markdown conversion so that they are easy to read quickly. Byword works quite well, as you can quickly toggle the preview of the formatted Markdown file for classroom purposes. It has an easy, fast sync; further, it's not a closed garden, in that the files are still TXT files and not a proprietary format. That's pretty close to what I was wanting, and so I'm experimenting with this.
The next stage for academicians is long text and professional writing, which Markdown is not designed for. Academic citations are fairly rigorous and need more robustness than even MultiMarkdown provides. Until there is a Markdown more oriented towards the printed page (or its simulacrum, the PDF file) instead of HTML – or, until academic writing becomes more fully web-oriented – Markdown isn't probably a good option for peer-reviewed works or manuscripts.