Zotero is a free, open source reference management software, for managing bibliographic data and related research materials (e.g., PDFs). Notable features include web browser integration, online syncing, generation of in-text citations, footnotes and bibliographies, as well as integration with the word processors.
Zotero Standalone allows Zotero to be run as an independent program outside Firefox. You can add PDFs, images, audio and video files, snapshots of web pages, and really anything else. Zotero automatically indexes the full-text content of your library. On many websites such as library catalogs, PubMed, Google Scholar, Google Books, Amazon.com, Wikipedia, and publisher's websites, Zotero shows an icon when a book, article, or other resource is being viewed. By clicking this icon, the full reference information can be saved to the Zotero library.
Zotero can also save a copy of the webpage, or, in the case of scientific articles, a copy of the full text PDF.