The Plague!

Shelley Batts has a great series on the Black Death, discussing what medieval medical plague doctors wore in an attempt to prevent infection, the most likely causative organism and mode of transmission (Yersinia pestis [AKA, bubonic plague] and fleas on rats, respectively), and alternatives to the Y. pestis theory. She also notes that plague is still a problem, as discussed in this PLoS Medicine paper; it has even led to at least one death in the United States.

Tara Smith provides more information on criticisms of Y. pestis as the causative agent of the Black Death, examines the validity of those criticisms, and discusses what the discovery of Y. pestis DNA in medieval mass graves tells us about the etiology of the Black Death.