Over the course of my graduate school career, I have used three of the major players in the reference manager game: Endnote, Refworks, and Mendeley. And to spoil the suspense immediately, Mendeley has been the clear winner for me.
What are some of my favorite features of Mendeley? I think my favorite feature is the interface for handling PDF attachments, especially the renaming of the files. Having the entire database synced with the Mendeley server is much better than keeping track of different Endnote library files. Mendeley also has deep integration with Overleaf, a web application that I do much of my writing in. And the base version of Mendeley is free, with 2 GB of database storage.
In last place is Refworks. My top complaint is that it opens far too many tabs. Every import creates its own tab. As someone who already has a difficult time not filling the address bar, this is quite an annoyance. Since Refworks is entirely a web-based application, they also have the difficulties of managing the appearance in different browsers and screen sizes, and in many cases my dialog boxes are cut off or awkward to use.
Endnote was quality software, but it was not free when I used it, and I didn’t care for managing the backups myself. The only other reference manager that I would try would be Zotero, which also shares several of the advantages of Mendeley.