AnkaSearch: "AnkaSearch is a Meta Search and Deep Web Search Desktop tool. Apart from searching for pages, AnkaSearch also enables you to save selected downloaded pages, organize and manage the saved pages." (Free, Windows)

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BASE: "multi-disciplinary search engine for academically relevant web resources." OAI service provider (Free, web-based)

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BlueOrganizer: "BlueOrganizer adds a button to your toolbar with a menu that has been automatically personalized based on your browsing history. This menu contains contextual shortcuts to make all relevant information for books, music, movies, wines, recipes, stocks, and more just 1-click away."  (Free, Firefox add-on)

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CiteULike: "a free service for managing and discovering scholarly references"--find scholarly resources other researchers have added to their bibliographies (Free, web-based) [review]

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DeeperWeb: Firefox add-on that provides faceted Google searches.  Offers a tag cloud view, blog search, search of articles and other resources, etc. (Free, browser-based)

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DOAJ: Directory of Open Access Journals, "The Directory aims to be comprehensive and cover all open access scientific and scholarly journals that use a quality control system to guarantee the content." (Free, web-based)

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Dispute Finder: Firefox extension that allows "activists" to annotate disputed claims on web pages and "readers" to see those annotations and discover other points of view. (Free, Firefox add-on)

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Freebase: "provides datasets about millions of things, from movies to dog breeds to beers of the world. These datasets are built by the community, for the community." (Free, web-based)

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Google Books: can search a large and growing collection of digitized books [review] (Free, web-based)

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Google Scholar: "can search across many disciplines and sources: peer-reviewed papers, theses, books, abstracts and articles, from academic publishers, professional societies, preprint repositories, universities and other scholarly organizations" (Free, web-based)

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Internet Archive: Offers extensive collections of texts, audio, moving images, and software as well as archived web pages .(Free, web-based)

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Library LookUp: "Bookmarklets for looking up catalog records from book-related sites."  (Free, bookmarklet)

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LibX: "a browser plugin for Firefox and Internet Explorer that provides direct access to your library's resources. " [review] (Free, browser plug-in)

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National Academies Reference Finder: "take a large block of text (from an article, a rough draft of a paper, a book chapter, a news story), and use it intelligently to 'find more like it.'" (Free, web-based)

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OAIster: "union catalog of digital resources...can be searched by Title, Author/Creator, Subject, Language or Entire Record"  (Free, web-based)

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Referencecenter.com: a mashup of various reference and research information that provides a deep dive into a given topic.

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Scholarometer: Firefox extension that supports citation analysis.  Offers a "smart interface" to Google Scholar. (Free, Firefox extension)

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SearchPigeon: search open access publications in the humanities (Free, web-based) 

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SearchTeam: collaborative search engine (Free, web-based)

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Worldcat.org: a union catalog that searches collections of over 10,000 libraries worldwide (Free, web-based)