Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Diigo - Diigo is a powerful research tool and a knowledge-sharing community
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
WorldBrains Memex - Bookmarking for the power users of the web. A privacy focused extension to annotate, search and organize what you've seen online.
Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.
EndNote - Accelerate Your Research. Save time, stay organized, collaborate with colleagues and get published with EndNote 20.