MPEZ  Using Bibdesk + Textmate + Latex for my science thesis. A little bit of a learning curve if you are new to these tools, but well worth it - so much more robust than the other options. The new features of Bibdesk such as being able to import references from webpages are welcome. A great product, just give it a little time.  
(Version 1.3.21)

MARK EVERITT  For some who use this it may be worth looking into CiteULike

http://www.citeulike.org/

It allows you to upload pdf files, and if you navigate to a journal's website you can automatically get all the details for the paper and it will assemble the bibtex for you. It's neat because I can get hold of my papers wherever I am and searching in it is nice too.

Before CiteULike I used JabRef a lot.  
(Version 1.3.18)

RCN  Perhaps the best designed Mac application there is. It's a shame that more people aren't aware of BibDesk and end up buying one of the competitors instead. BibDesk makes managing large collections of pdfs easy, and you don't need to know anything about bibtex to use it.

In fact, one of the best things about BibDesk is how well it integrates with Skim, the pdf reader/annotation app. Manage your database with BibDesk, double click on a pdf to open it with Skim, do all your highlighting and note taking, and when you go back to BibDesk your highlights and notes are waiting there as searchable text! In fact, it is simple to search across the entire text of a large library - searching both the text of the pdfs and your own notes.

The screenshot (maybe it is time for a new one?) really doesn't begin to show you how well this program is designed or all of the features (including integration with a number of online databases). If you're looking for anything near the bibliography/note taking realm, I strongly suggest you give BibDesk a try.  
(Version 1.3.16)

LUGAL  BibDesk is absolutely wonderful software, far better than any other BibTex manager I've ever used. I've been using BibDesk heavily for a few years (writing my dissertation), and the only problem that I've ever had was fixed by the developers on the same day that I reported it.

It's a deep program, with lots of features that I don't use, so it might seem a little overwhelming to the uninitiated, but it's so good that anyone who needs to manage a large bibliography--even if they don't use BibTex--really should try it out.  
(Version 1.3.13)

JOACHIMR  After using Endnote (when it was still a Mac product) and then Bookend and trying Sente, this is my absolute fav app, especially since it allowed me to toss Word. I use it for organize (very effortlessly) all my research and even my drafts in a Lyx - BibDesk combination. Perfect integration (as BibDesk basically edits the BibTeX file you need for Lyx). I strongly suggest for all folks who are frustrated with MS Word to give these two apps a try. Tons of other users are willing and able to support you and there's tons of information available on various user groups. I only wish that it would not have to index the content of PDFs each time you want to search (only one time until you close the app).  
(Version 1.3.21)

RAE  I was very happy to see a free app that dose the job as reference manage, however,it crashes easily. Just then I tried to use this app again to see if it had improved, but it crashed the moment I started. Thinking back, I still remember the frustration of needing to attach files by hand which bugs me when I have lots of PDFs. The worst thing is that when it crashes, I lost all the data I entered. T_T

Another minor issue: there is no scroll left or right when browsing a webpage.

If you have lots of articles and need to work with papers for a long time, Sente is better. Otherwise, this app should work as well.   
(Version 1.3.18)

FXT  it took me awhile to warm up to bibdesk,

but at this point i couldn't operate efficiently without it. a "must have" if you're into refereed journal literature.

are donations accepted?

fxt  
(Version 1.3.17)

OSOS10  A great program. Makes the annoying tasks of organizing references, referring to them from an article, linking them to the corresponding pdf files and urls a pleasure. Thanks ....  
(Version 1.2.9)

KLAGRECA  Am I the only one, or do "real" groups for organizing references a better idea than "virtual" groups?

(I'm talking about where all of the references reside in "All Publications" and groups contain only pointers to the reference.)

Otherwise, great program. When considering price, Bibdesk is better than Endnote by a long shot.   
(Version 1.2.9)

DFK  An excellent program -- powerful and flexible. The export options are particularly nice. Thanks to all who contributed!  
(Version 1.2.7)