Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
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.
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Docear - Docear
Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.
BibDesk - BibDesk is an organizational software created to help you edit and manage your bibliography. It keeps track of your bibliographic information as well as said information's associated web links and files. Read more about BibDesk.