Maybe it would be a good idea for all of us to share what freeware we currently use/endorse. Feel free to post yours in the comment section.
2. R through JGR (Jaguar) - I prefer to TinnR just because I like it.
3. JabRef - I can't say enough good things about this citation manager.
4. Zotero Firefox extension - This is a really easy way to get references in BibTex form. It does a great job of recognizing sources on a page full of things. Like an entire page of google scholar results or an amazon.com search.
Also, I'm sure almost everyone knows you can output references in BibTex format from googlar scholar (under scholar preferences), but if not, I thought it was worth mentioning.