It's a huge pleasure to review Bookends 12. It is an excellent update to a brilliant program.
I have extensively used/tried Endnote, Papers (Papers2, Papers3), Sente, Mendeley and others over the years. I have a large database of >11,000 references, many with PDFs linked.
I've therefore needed a flexible, speedy and absolutely robust database system for references, with easy importing and handling, and easy bibliography generation.
Bookends scores massively in all these areas. It is very fast, and lean on resources. It is bombproof, and crashproof (EndNote in my experience has always been dogged by crashes and awkwardness). Compared to Papers3 it is lightning fast on searches, finding references quickly and easily. It integrates well with word processors (though the Papers system of citing into any document is clever).
I like the flexible built-in browser, the new clip-to-bookends bookmarklet for when I forget to use the built-in browser, and the great PDF handling. It was always nice to display PDFs in the main window of bookends, and now being able to click on the 'paperclip' in the main ref window and launch straight into Preview or Adobe Reader is even better.
I also love the ease of customising reference styles. If I'm making a new output style for a grant or paper, it's easy and intuitive. Trying to do the editing for Papers2 and Papers3 took ages, lots of fiddling, and generally a bit of extra swearing. Bookends: quick, easy, obvious. Genius.
Above all else, it has Jon. The best support ever, the most responsive designer, and the most courteous service.
This really is the outstanding reference manager for Macs. It's been around a while, and others have tried to beat it, but in my experience none come close for speed, reliability, and overall performance. Version 12 has the added advantage of being simpler in layout and look, and a pleasure to use.