GanttProject is a cross-platform desktop tool for project scheduling and management. It runs on Windows, Linux and MacOSX, it is free and its code is opensource.
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.