MediaWiki - MediaWiki is a free software wiki package written in PHP, originally for use on Wikipedia.
Mendeley - Easily organize your papers, read & annotate your PDFs, collaborate in private or open groups, and securely access your research from everywhere.
TiddlyWiki - a non-linear personal web notebook
Zotero - Zotero is a free, easy-to-use tool to help you collect, organize, cite, and share research.
Confluence - Confluence is content collaboration software that changes how modern teams work
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.