Pybliographer is one of those programs that belong to every E2 noder's toolbox (provided they're using *NIX of some sort). I've noted my reference citations suck without this nifty little app. I noted I once again need to go through many recent nodes of mine and add sources. I bet "FRCS" isn't enough of a source reference. =) Anyway, I'm digress..
Pybliographer is an application that makes reference lists quite easy. It maintains a database of citations, and is able to store this database in the de facto standard format of citations - the BibTeX format. It also handles some other formats I've never heard of (ISI, Ovid, Medline, Refer).
Under the hood it's a Python package for all kinds of reference handling, editing and formatting, but there are also front-ends for it so that people could actually use it (duh!) The package comes with both a textual interface and also a GTK+/GNOME GUI (Pybliographic).
In my opinion it has a great feature that makes it extremely worthy: It has XML formatting language with which it's pretty easy to construct various kinds of HTML (etc) output formats. I can pick my references from a list, hit "Format", select my formatting file and output file, and *boom* it produces neat citations that require very minimal editing. (I may release my E2 format xml one day, too.)
Along with HTML generation, it also interfaces with LyX pretty nicely from what I've heard.
Of all reference managers and formatters I've used on GNU/Linux, this is definitely the best I've seen. I particularly like the BibTeX compatibility and neat output formatting.
Home page: http://pybliographer.sourceforge.net/ - Also available as a Debian package.