Bsag over at But She’s a Girl has a nice post on using Org mode and Pandoc. She says that she’s abandoned Markup in favor of Org mode because, among other things, it provides a rich set facilities for handling the structured text. You can move headers and their associated trees up or down and you can promote or demote them in the hierarchy. And, of course, it has especially rich table editing capabilities. Markup is wonderful and all—I mean that—but if you’re using Emacs as your editor, Org brings you everything Markdown does and much more. You really should be using it.
I’ve written extensively about my own system of using Org mode for writing. Normally, that means I write in Org and then export to HTML, PDF, or this blog. I use the native Org exporters for that so I don’t usually need Pandoc. Bsag, has gone another route and uses ox-pandoc as her export engine. That means that all the conversion is done by Pandoc. I don’t know if that’s better or worse than my system but if you’re just getting started you might want to give bsag’s systems a try.
She also mentions using Org and Pandoc to implement a lab notebook. If you’re working in the sciences and need to keep a lab notebook, you should definitely give her post a read.