Some other tools, that don't (yet) fit into any of our categories:
The Bazaar Online Conference system is a promising-looking open source (i.e. free) online course management system that includes collaboration features such as discussion tools. It is described here and this is the home page. Some features: file upload and download, chat, polls, newsgroups.
Colloquia is a very interesting groupware product that runs off-line, with new messages, groups, resources, tasks etc. automatically updated via e-mail when a user goes online. Free for non-commercial educational use.
The Digital Document Discourse Environment is a "tool for document-centric discussion", used amongst others by the journal Discourse Analysis Online (the easiest way of seeing what it can do is to check out the journal). It breaks structured documents (such as most academic papers) into html chunks, each of which can then be discussed (e.g. by reviewers).
Some other interesting other categories of collaboration tools:
Annotation tools (where you can see notes left by others in your group when you visit a website)
Granular addressing systems, such as PurpleSlurple which allows one to povide a link to individual paragraphs within any web page.