MacResearch

Of course, BibDesk [1], powerful BibTex-based reference manager with integrated PubMed reference access support, a wide rage of export formats [2], and local and remote PDF linking… which you can combine with Skim [3] for annotations. It can also read ISI and JSTOR file formats.

And both BibDesk and Skim are open-source and free.

[1] BibDesk: http://bibdesk.sourceforge.net/

[2] Supported export formats: BibTeX, RIS, HTML, MODS XML, EndNote XML, Atom XML, RSS, Amsref LTB, RTF, RTF packages with graphics, Word .doc

[3] Skim: http://skim-app.sourceforge.net/

Note that BibDesk can link to and search contents of any file, not just PDF! Further, you can search PubMed, Web of Science (in nightly builds), and z39.50 databases from within BibDesk.

It also supports Refman, MARC, MODS, RIS, and Dublin Core XML formats for import. Disclaimer: I'm one of the developers of BibDesk.

I must say I really like bookends. Coming from using endnote, bookends is speedier, is more stable and has better options for my type of work. I tend to read my papers in Skim and then attach them into my bookends reference, so they're there for the next time. I also take more extensive notes in bookends. It has a very good search engine and is very modifiable.

Also, I think if you're a student, you can buy bookends for 69 dollars.

http://thirdstreetsoftware.com

better than the free ones and the demos I tried... (not all of those listed however)

you should at least add it to the list.

the group is very response to private email and feature requests.

Edd

It'll import BibTex, endnote 9 , XML, pubmed, refer(generic), refer(endnote) automatically.

It'll organize pdfs, images, or any other file automatically with a renaming scheme that's fully customizable for each record with drag and drop

It'll search pubmed, web of knnowledge, SRU and Z39.50 data sources (local and national libraries with a few preset) saving and updating the searches until you delete them

It allows easy annotation on records of books, articled, interviews etc. and simple creation of records

but the best thing is how spotlight works with it. Spotlight searches the abstract and the pdf and links to the sente reference record

word integration is good but is menu not toolbar yet.

I work as a PhD candidate in physiology , but can't imagine not using this in a large number of files, plus students get it for $90

I want to jump on the BibDesk bandwagon, but I think it's important for somebody to say that in addition to being powerful, it's also easy. I'm brand new to it after one too many Endnote freezes over the weekend, and I'd never heard of BibTeX/LaTeX, and have only very basic coding experience, and I was still up and running with a very steep (meaning short) learning curve. In addition to a pleasantly iTunesey interface, the integration with Skim is great, and the integrated search and importing from PubMed is great. I have a roll-your-own pdf-management system based on spotlight tags and using Path Finder for previewing, smart folders for searching/organizing, etc., and BibDesk integrates nicely with it, in the sense that it could replace it over time as I actually cite papers without requiring a bunch of work from me up front. In short, it is the best thing since sliced bread. And free. And I am not, nor am I sleeping with, anyone involved in its development, for the record.

Sente would be similarly great, even if less free, if it actually did quickly what it appears to be able to do. But it took me about half an hour with the trial download to get weary of search results that ignored my modifiers, and spinning beachballs of death appearing for every little thing I did. To be fair, I'm working in Tiger on an older machine (G4), so Sente's poor performance for me may be attributable to that (and I suppose there's always the possibility of cockpit trouble).