Common file-formats for writing research papers This is a rewrite of a question that was perhaps-naively posed. I rephrase...

What file formats are ok/good/ideal/common/long-term-viable/archivable/useful for research papers?

And, also, there's the history-question:

What is the story of viable file-formats in the last 20+ years?
plain text/markup language

For mathematics, I think TeX/LaTeX is the way to go.  This is the standard way to write papers in nearly all areas of math (perhaps not biomath, where collaborators necessitate Word), so there's little extra cost.  One advantage of this approach is that it's easy to automate outputting in almost any format you want.  Furthermore, as new formats develop, we will almost certainly develop tools to convert TeX source to these new formats.  The arXiv is a great example of this model.