Check out Mendeley, ReadCube and Citavi.<p>ReadCube (www.readcube.com) is focussed on organizing your personal library, though it also has an inbuilt PDF viewer with annotation capabilities and a browser for searching PubMed, Scholar et al. It is cross-platform: Windows, Mac, mobile - not Linux though. A very nice interface and the basic version is free. The Pro license brings you cloud storage and syncing.<p>Citavi (www.citavi.com) is probably the ultimate desktop software for managing scientific literature. Apart from organizing your library, annotating PDFs and writing notes, it also has plenty of tools to help you write your own articles. Unfortunately, it only runs on Windows and comes with a hefty price tag (though many institutions have a site license - check if you are eligible).<p>Mendeley (www.mendeley.com) might be the best choice for you. Like ReadCube, it concentrates mainly on library management and paper annotation. However, it also provides plugins for browsers and word processors that add some neat functionality (such as automatic citation insertion for LibreOffice). It is multiplatform (Windows, Mac, Linux, mobile) and free. Syncing is included in the basic free plan, the premium plan gives you more storage space and teamworking functions.<p>Sadly, none of the above is open source, and only Mendeley works on Linux. Otherwise, take your pick :-)