I've used most of the major citation managers: RefWorks, Flow, EndNote (web and client), Zotero, Mendeley, ProCite (remember that one?). I've looked at Papers. I've dabbled with BibTex using a couple of different tools. I've watched the videos on the new RefWorks 3 coming out. I've given training on RefWorks and EndNote... and I'm frustrated.
Almost all of these have the model that you are one person, with one field of research, who will continue to use the same somewhat limited number of references over the many years.
As a librarian, I like to compile references for people into RefWorks collections and then turn them over. I've done this by setting up new accounts for them. This will not be possible in the new version in which there's only one account per e-mail. Sharing folders doesn't work because I don't want my dissertation and professional work database to be crammed with thousands of unrelated articles.
I have tried to collaborate with people in Zotero and I can't seem to get rid of a thousand or so articles that were relevant to a project from several years ago.
Further, they only get worse at deduplication. I use a citation manager to compile references and deduplication for bibliometrics. RefWorks chokes when your database gets above a few thousand. Plus, it's not configurable. You can't say ignore title, just look at year, authors, publication or something like that. Or only look at title. You can't review duplicates, find that they're part 1 and part 2 or conference presentation and journal paper, and then have them not show up every time. These are really not intended for my uses.
So I'm going to go back to trying client software. First I'll try a EndNote X ( an ancient copy that has been sitting here in a box still sealed). Then I'll probably go to BibTeX, maybe using SVN, and maybe using code for some of the tricks. Why should I have to?
And that's another reason to get my @##% dissertation done while RefWorks and the Word plugin still work on my home computer.