I’m a big fan of markdown (md), and especially of Fletcher Penney’s branch multimarkdown (mmd). John Gruber invented the project to make it easier to write pieces destined for HTML, such as blog entries. md and its variants essentially provide a very light markup for plaintext that is transformed by the markdown engine into HTML. This post was written in mmd in textmate, and transformed/published using a python implementation of md. It’s so convenient that it has seriously taken off, at least in the Mac world, and most good text editors have md support baked in with syntax highlighting. But, it’s not just text editors (which you should be using to make your files anyway), as Scrivener has mmd support built in. And, enter lately a whole host of small and specialty apps for iOS and OSX systems. For example, I absolutely love Brett Terpstra’s fork of Notational Velocity, nValt, which includes several built-in mmd features including a preview pane for mmd-formatted notes, as well as browser plugins to import web pages directly into nValt transformed into md files.
Terpstra is also responsible for another of my favorite little apps, Marked. Marked is, essentially, a universal previewer and exporter for md and mmd files. The simple idea is this– if you’re working on a file, you can simultaneously open it in Marked to see a live preview of what it will look like converted into HTML. The power, though, is this– you can take that file and save it directly into not just HTML, but also to RTF or PDF. Moreover, using custom CSS, you can control directly what the output looks like, essentially giving yourself typographical control over your documents. I set up a custom CSS sheet that uses Adobe Garamond Pro (my absolute favorite font for academic writing output). So, now I can write anything I’m working on– be it a blog post, note-taking for research, transcriptions of my documents, letters of recommendation, my c.v., and even formal papers or chapters in my favorite text editor (textmate) using mmd and have easy export to RTF (if I need to share them with a Microsoft Word user) or PDF (if I don’t). Moreover, the files are simple plain text files, which are small and easy to version control. I can write, if I want, custom CSS for any task, and have real control over the PDF appearance of my documents without the complexity of writing LaTeX. And if need be, I can easily import into Scrivener for serious writing.1 And here’s a footnote on footnotes.2
Given the ability make footnotes, control headings, automatically produce a table of contents, and, with custom CSS, control typography, it’s hard to imagine what I can’t do with (multi)markdown as an academic with a whole variety of writing needs.
Associate Professor of Early Latin America Department of History University of Tennessee-Knoxville
parezco y digo 
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How do you deal with citations in html exports?
I found pandoc’s CSL approach to be fantastic, however, pandoc’s markdown does not handle figure nor table references.
I feel like the markdown to html or latex approach to be a fantastic way of writing. However, the two main implementations are lacking in some small, but important ways.