If you would like your students to discuss and annotate documents online in a way which allows rich conversations to develop, NowComment may be the tool you are looking for.
NowComment is a web application designed for group collaboration, discussion, annotation, and close reading of online documents. It encourages rich, in-depth conversations by showing threaded comments “in context” with the original document. Group members start or join conversations on whatever passages they find interesting and important, intellectually engaging with a text (and with each other) in ways that can extend or take the place of face-to-face class discussion. Instructors can join in to steer the discussion or correct errors, and a transcript is automatically created for grading and student review. Take a look at the two-minute video overview, or explore a sample document.