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HTTrack - HTTrack is a free (GPL, libre/free software) and easy-to-use offline browser utility.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
WebCopy - Cyotek WebCopy is a free tool for copying full or partial websites locally onto your harddisk for offline viewing.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
SiteSucker - SiteSucker is a Macintosh application that automatically downloads Web sites from the Internet.
Qiqqa - Qiqqa is a free research and reference management software. It can be used in many organizational projects from the academic to the personal to the business endeavor. Read more about Qiqqa.