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Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
Aigaion Reference Management System - Aigaion is a bibliography management system that seems to be the perfect tool for managing your bibliography and references.
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.
ProCite - ProCite is a tool for creating citations according to the standard defined by the users.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Papers by ReadCube - ReadCube Papers is a sumptuous reference manager helping out academic writers to get the most out when it comes to access and discovering more citations with multiple libraries or databases.