If you are interested in annotations on ontologies or any other sort of resource, check out the W3C Project Annotea. They are working towards making it possible to load annotations alongside any web resource. Imagine going to a web page, and clicking on a toolbar button to reveal annotations made by any number of people across the world. I assume some other mechanisms would be necessary to make sure the annotations, bookmarks, and marginalia were relevant to you, but you get the idea.
They have built an annotation schema for describing the RDF structure of those annotations, and some basic software for creating annotations and storing them on an annotation server. The mozilla project is hosting Annozilla, an attempt to integrate Annotea into mozilla and firefox.
Each annotation can then become a discussion thread of its own. Imagine reading a web page on history, and noticing that someone else has posted an annotation that suggests a linkage to some other event that happened in history. You would then be able to reply to that annotation, ask a question, or dispute its accuracy.
In these kinds of discussion, the discussion’s context would be extremely localized. An entire thread of discussion might take place about a particular phrase or passage in a document. Such discussions have always taken place, the difference is that with stored annotations, there is explicit traceability back to the source data that provides “context” for the discussion. Of course you’ll always have issues such as when the discussion topic drifts. Still, tracking the seed idea or piece of information that started the discourse has its own benefits.