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

EasyBib - Automatic works cited and bibliography formatting for MLA, APA and Chicago/Turabian citation styles.

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

Paperpile - Clean and simple and reference management for the web. Sync your PDFs to Google Drive and cite your papers in Google Docs.

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.

Citavi - Citavi is a program for Microsoft Windows that manages literary references and organizes organizational knowledge.