[GlennS]

The first thing you need to know about is http://johnmacfarlane.net/pandoc/ which is a fantastic tool.

So I would say that it might be worth reconsidering LaTeX because it has http://www.bibtex.org/ which is excellent for academic papers. The investment to get competent with LaTeX is certainly several hours, but it pays itself back quickly. See http://en.wikibooks.org/wiki/LaTeX for a good learning resource.

For myself, I mainly use http://orgmode.org/ for emacs. This can export as LaTeX, and from there to any of the vast multitude of formats that LaTeX can be converted to. However, if you're not willing to learn LaTeX, then you're probably not willing to learn emacs either: where LaTeX is a matter of hours to learn competently, emacs takes weeks.

I used Markdown to write the bulk of my text for a while, but I found it didn't scale very well to large documents. It is great for blog posts and the like.

[xorbyte]

MultiMarkdown might be more suitable for large documents, as it allows the inclusion of files between documents, cross-references etc.

[indralukmana]

thank you very much for the recommendations,

>>I used Markdown to write the bulk of my text for a while, but I found it didn't scale very well to large documents. It is great for blog posts and the like.

what do you use for large documents? does it have references /bibliography supports?