I'm not AS concerned about something like Ebola, because while being horrible, it's horribleness is self limiting because people die (relatively quickly) before they can spread it too far.
On the other hand, weaponized vCJD could have a population die off en masse years after they're infected. Since it can be transmitted via blood transfusions, it'd essentially shut down blood donations (although if everyone had it, I guess that wouldn't matter). Also just the fact that prion diseases can cause psychological symptoms make the implications different from something like a classical infectious disease.
Maybe the infection could use genetic mechanisms so that the infected pass it on to their children. Maybe this already happened thousands of years ago. X-Files Theme.