Fellow academic org-writers unite! Org is a great place to write papers. Unlike Markdown, which some people present as another alternative, Org supports cross-references. Also, being able to do complicated stuff by dropping back to LaTeX is a boon.
Because org-mode targets far more than than LaTeX/PDF in its standard case, isn't itself Turing complete, and supports vastly more stuff including literate programming in a huge number of languages.