I'm at a university that had WebCT, which then morphed into Blackboard and has just recently been replaced with Moodle. Having using those systems, both as a student and in teaching roles, I have to say that Moodle is just plain better. It's cheaper (TCO), more versatile and more usable. And much less prone to inducing rage :-)
Of course, that doesn't mean that it's invulnerable to screw-ups. If you lock it down from on high with One True Way of Using The System, then you're probably not going to suit the needs of different academic departments and their different kinds of students (CompSci versus English majors, for example). On the other hand, too little structure can lead to ongoing support problems in security, maintenance and training/helpdesk services. The trick is to find a balance that works across your institution.