How about antibiotics-which are a good thing and have saved tons of lives- when overused give rise to a super-resistant bug that will wipe out large numbers of people? Sounds like a "B" Sci-fi Japanese flick from the 60s, but it's possible and even likely at some point.
I only started looking seriously at this after getting lyme-disease which, ta-dah, is requiring me to take mass quantities of antibiotics for a while.
Thomas