DEVONthink and Bookends work nicely together: DEVONthink Pro and up come with a smart template for quickly linking to references in Bookends, accept references dragged over from your collection, and Bookends can store “item links” for any document in DEVONthink. Just recently Sonny Software released Bookends 12 with an exciting set of new features. Check it out!
PS (1): If you had already downloaded Bookends 12 and it broke the drag-and-drop feature with DEVONthink please simply re-download it. Sonny Software have fixed this issue with a silent update.
PS (2): The next release of DEVONthink Pro and up will offer even better integration with Bookends.