Qiqqa is by far the strongest solution for research and managing pdf's. Zotero, named as a comparison is weak as it does not allow pdf;s to be loaded into its interface - you need to use a pdf reader, which defeats its whole purpose. With Qiqqa documents in a library can be searched together. It has excellent maps of your libraries. It is not prefect, having a few glitches, but still is the only one of its kind.
TagSpaces - TagSpaces is an open source platform for personal data management. With TagSpaces you can manage and organize the files on your laptop, tablet or smart phone.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
TagFlow - TagFlow is an intelligent files manager that use tags for organize your documents.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Tabbles - Tabbles use tags to organize and find files along with your colleagues.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .