http://www.openplans.org/projects/yucca/related-technologies/edit

• Annotea W3C standard for specifying annoations using an RDF based schema
• Connexion's implementation of Annotea
  
• Stet FSF commenting software, used for GPL3 commenting
• Commentary - Ian Bickings Paste commenting system 
  
• CommentPress Future of the book UI mockups, with a wordpress backend (formerly known as N-Dimentional) 

• Django's Comment System - Django framework's paragraph level commenting system

• Fleck - Commercial, free of charge web service for textual annotations