Dominik Brettnacher has released Annotate 0.1.6, a free annotation tool for DocBook documents. Based on an extension of the DocBook XSL and a DBMS to store the annotations, it looks to be very useful! There is also an online demo you can try. For more info, check out: http://www.brettnacher.org/annotate/.
Annotation has been added to DocBook v5.0, and is described here: http://docbook.org/tdg5/en/html/annotation.html