Substance is a fully web-based document authoring and publishing platform. With Substance, writers, journalists, scientists and everyone else who's interested in publishing can use an open platform for writing and sharing articles.
Foswiki is a wiki, so you and your team members can collaborate and edit pages directly in the web browser. For advanced collaboration, Foswiki lets you enter macros (similar to Excel) to automate pages and build entire applications from within your browser.
CommentPress is an open source theme for the WordPress blogging engine that allows readers to comment paragraph by paragraph in the margins of a text. Annotate, gloss, workshop, debate: with CommentPress you can do all of these things on a finer-grained level, turning a document into a conversation. It can be applied to a fixed document (paper/essay/book etc.) or to a running blog.