Top Choice: Sente
Sente has a beautiful interface, its fairly easy to add references (esp with its own browser), and hierarchical tagging is phenomenal for managing your entire library. Of course, its not perfect and, as a result, I still try to test the major new releases of its competitors. But I haven't seen enough to make me change yet. Some really like to highlight and annotate with Sente as well, but I've never liked that part of their software.
Last updated: 5.6.2013