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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.
PDFCrowd - Pdfcrowd is a Web/HTML to PDF online service. Convert HTML to PDF online in the browser or in your PHP, Python, Ruby, .NET, Java apps via the REST API.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
DocRaptor - As the only API powered by the Prince HTML-to-PDF engine, DocRaptor provides the best support for complex PDFs with powerful support for headers, page breaks, page numbers, flexbox, watermarks, accessible PDFs, and much more
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
PDFShift - Convert any HTML documents to high-fidelity PDF using a single POST request