Future of the Book has a Commentpress page. It looks interesting and serious.
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.