The Public Knowledge Project (PKP) is a multi-university initiative developing (free) open source software and conducting research to improve the quality and reach of scholarly publishing.
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.