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.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Adobe Acrobat DC - Make your job easier with Adobe Acrobat DC, the trusted PDF creator. Use Acrobat to convert, edit and sign PDF files at your desk or on the go.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
PdfHighlights - PdfHighlights extracts and exports all your PDF highlights and PDF annotations from all your PDF files into a single report.
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
DocMadeEasy - Edit and sign PDF. Send files safely and securely using end-to-end encryption with 256-bit AES. PDF document management and conversion.