I just started playing with this, and already I love it: Zotero. It’s like a bookmark manager crossed with a note-taking program crossed with BibTeX.
Zotero is an extension that runs inside Firefox 2.0 — click the icon, and it captures a complete bibliographic record of the page you’re looking at, and saves a copy. This is vital when you need to cite web pages that may not be permanent.
Even better, it has scrapers (they call them “translators”) for a bunch of online databases, the kind you get in university libraries. Say you’re reading the online PDF version of an article that appeared in a journal. Click on Zotero, and it saves the PDF then stores both the URL and the journal name, volume, number, page, author, title, etc. Then click another button and it spits out a bibliography in APA, MLA, or Chicago form.
It works for offline resources too. Look up a book in a card catalog, and click to record the bibliography. Add your own notes and links to files on your hard drive. Of course, it has a search function, with tagging promised in future release. It’s open-source.
Unlike the cool-but-geeky note-taking programs (like desktop Wikis), Zotero is designed for scholarly work, and it has some big-name research institutions behind it. Here’s hoping it continues to grow.