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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.
HTTrack - HTTrack is a free (GPL, libre/free software) and easy-to-use offline browser utility.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
SingleFile - Save a complete page into a single HTML file
JabRef - Graphical Java application for managing bibtex (. bib) databases.JabRef · JabRef Help · JabRef | Blog · OpenOffice/LibreOffice .
Web ScrapBook - A browser extension that captures the web page faithfully with highly customizable configurations.