When I evaluated Blackboard, WebCT, and Prometheus, I found all three to be pretty weak. Blackboard was the worst by far. WebCT had a huge number of features, but the seem to have been thrown in willy-nilly with very little intelligent integration. Prometheus was the best of the three in that the design seemed to value quality of implementation over number of features, but it had a lot of weaknesses too. It had relative links, making tie-ins to specific threads impossible, and no decent user profiling capabilities. (I seem to recall a problem with email alerts too, but it's been a while since I looked at it.)
Anyway, Prometheus was bought by Blackboard, so I don't know how much life it has left in it.
