I've written previously about John Kitchin and how he uses Emacs and Org mode for reproducible research. Kitchen is a researcher in Chemical Engineering from Carnegie Mellon University so he writes a lot of technical papers and he uses Org mode and Emacs to prepare them. You can watch the video that I linked above to get an idea of how he uses them to integrate his research notes and calculations into the source file for the paper.
If you've written or read any research papers from any scientific field, you know that they typically have citations to other papers and internal references to tables, figures, or other parts of the paper. Org can handle a lot of that—especially the internal links—out of the box and there are external packages to help with the bibtex tools.
Kitchin has written an Emacs package,
org-ref, that integrates these functions in a consistent way. He describes the package in a blog post on his group's site. If you write research or technical papers that have a lot of internal/external references you should take a look at the package to see if it can help you.
Kitchin says that the package currently works well only for LaTeX export but suggests that he will be adding support for other formats such as HTML in the future. Right now the package isn't in ELPA and he doesn't say whether he will place it there but it is available from his site: see his blog post for the link.
I hope he continues work on this package. It looks as if it could really make handling bibliographies a lot easier.
Update: Apparently, Kitchen is continuing work on
org-ref. In a subsequent post he describes how to export to other formats and remarks that export to HTML is working pretty well now. If you're interested in using Emacs to handle bibliographies, you should take a look at Kitchen's blog. He has many posts describing the work he's done in that area. It's pretty impressive.