Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.

Diigo - Diigo is a powerful research tool and a knowledge-sharing community

Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.

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.

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.