BibDesk: "BibDesk is a graphical bibliography manager for OS X, providing powerful BibTeX file management for Mac users." (Free, Mac)

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BibMe:  online bibliography-maker generating MLA, APA, Chicago and Turabian citations (Free, web-based)

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Bibus: open source "bibliographic and reference management software" that is designed for collaboration, hierarchical organization of resources, and live query of medical databases, such as PubMed (Free, cross-platform)

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Bookends: reference manager with support for retrieving bibliographic information and related files from the Web, automatically generating bibliographies, etc. (Commerical, Mac)

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Citeline: "a service to facilitate the web publishing of bibliographies and citation collections as interactive exhibits and facilitate the sharing of this type of data."  Can import Zotero and BibTex files. Part of MIT's Simile project. (Free, web-based)

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CiteULike: "A free service for managing and discovering scholarly references...[used] to organise your academic papers." (Free, web-based)

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Connotea : "Free online reference management for all researchers, clinicians and scientists" (Free, web-based)

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EndNote: "Web-based tool for managing and citing references in papers and creating bibliographies...integrates the following tasks into one program: Search bibliographic databases on the Internet; organize references, images, PDFs and other files; construct your paper with built-in manuscript templates; watch the bibliography and figure list appear as you write" (Commercial, web-based)

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Heurist: a collaborative academic bookmarking, bibliographic, and general database with rich data types, annotation, record interlinking and publication capabilities, including bibliography output and citation within Word. Reference import and bookmarklet. (Free, web-based)

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JabRef: "bibliography reference manager" that generates BibTeX files (Open source, cross-platform)

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Mendeley: "Free social software for managing and sharing research papers. It is also a Web 2.0 site for discovering research trends and connecting to like-minded academics." (Free, Windows/Mac/Linux)

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MyPeers: "follow your peers and get notified when they publish new works"; access publications; measure impact (Free, Mac)

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NoodleTools: MLA, APA, Chicago, and Turabian integrated citing and note-taking teaching software which prompts for analysis of source types and is unique in offering personal help on any citation.  Instructor/librarian view allows teacher to comment on work-in-progress providing just-in-time feedback in-context (Free and Subscription, web-based)

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OttoBib: allows you to enter an ISBN number and receive a formatted citation (Free, web-based)

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OWL at Purdue: a reference site, maintained by Purdue, which provides the user with many of the style guidelines listed in the handbook of the Modern Language association (Free, web-based) 

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Papers: "Papers bundles all the great technologies that come with Mac OS X to give you a completely new workflow for reading scientific articles. You seek, download, archive, and organize all your articles within a single application. But that is just the start, using spotlight you instantly find the paper you are looking for. Read it fullscreen, add your notes, send a copy to a colleague..." (Commercial, Mac OS X)

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Qiqqa: Manage, annotate and tag PDFs; sync collections (Free, PC)

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Referencer: "a Gnome application to organise documents or references, and ultimately generate a BibTeX bibliography file" (Open source, Linux)

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RefWorks: "RefWorks -- an online research management, writing and collaboration tool -- is designed to help researchers easily gather, manage, store and share all types of information, as well as generate citations and bibliographies." (Commercial, web-based)

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Sente: "Sente 5 is the next-generation academic reference manager. Sente helps you find, organize, review and cite the academic literature in your field, and it does it in ways that you have probably not thought possible before. Sente also helps you build and maintain your library of PDF files for these references. .Sente also excels at properly formatting bibliographies in your papers" (Commercial, Mac)

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Zotero: "web-based  extension to help you collect, manage, and cite your research sources", compiles a library that can be accessed remotely (Free; Windows/Mac/Linux, requires Firefox browser)

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