LimeLite - A simple, easy-to-use annotation tool for Mac
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
LightTag - The text annotation tool for teams
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Good Annotations - A online annotation tool that is perfect for providing feedback to your team.
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.