Bryan Roberts over at Soul Physics has an interesting Githup repository, called Emacs Zen, that shows how to set up Emacs on OS X as a LaTeX/Markdown/HTML/CSS/JavaScript system. If you want an Emacs installation geared for writing, his repository has all you need. He also has directions for getting and installing Emacs and the necessary packages such as ACUTeX. He mentions the PDF viewer skim, which, he claims, makes syncing with Emacs particularly easy.
The only important thing he doesn’t mention is Org mode. If you collaborate with colleagues who aren’t Emacs users, markdown may make some sense but, really, if you want to do your writing with a lightweight markup language, Org can’t be beat. Many researchers will automatically fire up LaTeX for their journal papers but as John Kitchin has shown, you can write in Org, import the journal style sheet, and export to journal-quality LaTeX.
Of course, you can use Roberts’ setup and still use Org mode so if you’re looking for an incredible writing system, his repository is worth taking a look at.