As reported in this Campus Technology article, Carnegie Mellon University has started using a product called Classroom Salon to encourage collaborative reading and commenting. This seems like a very effective way to share comments on specific passages in a text, either assigned by the instructor or submitted by students themselves.
I think that such a process is probably very effective, and would benefit from being more largely applied to electronic textbooks and other learning objects of different forms (think Youtube or Flickr annotations, for instance). Academic reading is about finding sentences that raise questions or make students think of something else that is related, so this system is perfect for those tasks.
Institutions can request access to pilot, but it doesn’t seem like the software itself will be made available as open source from what I have seen, which is a shame.