There’s a whole world beyond RefWorks and Endnote. This Lifehacker post provides suggestions for well over a dozen different reference managers.
As a BibDesk user myself, I often wonder whether we as librarians should be doing more to support reference managers, especially Zotero and some of the other free options out there that would be beneficial to those who don’t have access to discounted or site licensed commercial products.
Good question, though I’d remove the qualifier at the end, which is how commercial vendors would like to frame the issue (”yes, you can use free alternatives, but if you want the best software, pay for it”). The promise of tools like Zotero is the same promise as Firefox: not only free, but better. As a former Endnote user, I have every faith that Zotero will realize that promise.