Like many people who write in LATEX, I use BibTeX for automatically generating bibliographies. I used to manage the databases by hand, but after writing several papers that needed similar references and dozens of papers in the database, this gets a bit unwieldy.
JabRef has a rather friendly interface, can manage several databases at once, copy between databases, and can import and export a number of formats. It can also import data from CiteSeer and PubMed. This means that once you have researched a paper on either of those two repositories, you can import the bibliography data by simply entering the reference in JabRef. You can also copy the citation command to the clipboard, or insert it directly into LyX.
The entry format is customizable, so you can add new entry types or add new fields to existing types. If you enter a URL for a paper, you can open it in the web browser with one click; if you enter the path name of the corresponding PDF file, you can open that in a viewer. This makes it the poor man’s document management system.
I usually don’t rely on GUI tools very much, but in this case, it seems worth it. I think JabRef is going to make managing my references a lot easier.