Academic papers in Linux
We're beginning to put an academic paper together, and of course I'd like to do this using open-source software if I can. My PI (principal investigator, the head of the lab) uses Word — so whatever ends up getting used, it needs some capability to at least export to .doc or .rtf. A critical aspect of any solid academic paper is citing your reference in a bibliography. OpenOffice.org does have some basic bibliography capabilities, but that's what they are: basic. Work is underway to fix that, but it's not expected to get anywhere for a year or so.

After some research, I've come across a few promising packages:

Zotero: A Firefox 2.0 extension, public beta started less than 2 weeks ago. No integration with word processors yet, but you can copy and paste a formatted bibliography across, and export and import the actual data. "It lives right where you do your work — in the web browser itself." As a result, adding references from online searches such as PubMed is as simple as a single click. Every other package needs explicit support added for online searches.
Bibus: Uses OpenOffice.org's Python functionality, also integrates with MS Word. The build system sucks — it should use distutils, but instead it's got some custom Makefile and weird shell scripts and configuration files. Its functionality comes highly recommended, however. Will do PubMed and eTBLAST queries.
Pybliographer: The development version (1.3) integrates into OO.o and LyX. The 1.3-series GUI is alpha-quality and just had its first release. Will do PubMed, Web of Science and CrossRef queries.
bibutils: Command-line filters to convert between a variety of formats, including EndNote (which is currently in use under MS Word). Also handles RIS and BibTex, so that provides for OO.o import and export as well.

Update: As of now, bibutils and Bibus are both available in Portage. Try 'em out.