Blackboard's real threat is open source. By filing a patent infringement lawsuit against Desire2Learn Blackboard has at the same time fired a shot across the bow of open source projects such as Moodle, Sakai, and .LRN, which are slowly emerging as disruptive innovations in the elearning space. In the long run Blackboard knows it can't win on product quality or innovation. Therefore, it will exploit patents as its WMD.
What is Blackboard's diabolical strategy to crush open source?
I don't believe they will directly go after open source projects. They don't need to. Blackboard just needs to create enough FUD among lawyers, whose entire frame of reference is built around litigation avoidance, so that new institutions interested in adopting an open source solution just won't go there.
Here is a likely conversation during the contract stage:
College X Faculty & CIO: "We want to use Moodle."
College X General Counsel: "We can't use Moodle (or Sakai or...) because WE risk exposure to a patent lawsuit by Blackboard. We don't have the resources to fight it even if we ultimately were to win. Counsel's recommendation is that you find an alternative."
What CIO in their right mind will risk career suicide by going against Counsel's advice?
In order to "win" against open source Blackboard doesn't need to sue existing users or go after open source projects. (It doesn't mean they won't). It just needs to create the Fear of Patent Ligitation among potential adopters. By suing Desire2Learn it has achieved that objective. If your competition can't get any new business, you have effectively eliminated them.