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.
Moodle is similar, but runs online on a server.
An interesting class of collaboration technologies is journal management systems, of which there are many commercial and open source examples available. One such system is the Open Journal System, which is open source and "assists with every stage of the refereed publishing process, from submissions through to online publication and indexing." They also have other free software downloads and demos. See also The Deconstructed Journal - a new model for Academic Publishing by John W T Smith. Another free online journal management system is provided by the International Consortium for the Advancement of Academic Publication. There is also the commercial Online Journal Publishing Service (OJPS).
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:
Also consider conference calls, chat rooms, and shared acoustic spaces.