I don’t know how many ion motors have flown, but they seem to run forever and get no respect since they are quiet and low impact. Ion motor tech will open space to resource development once the Treaty is repealed.
Deep Space One was flown by NASA as a test bed which included proving the Ion Engine and the Japanese currently have Hayabusa on it’s return trip to Earth, hopefully with some asteroid soil samples. ESA flew one last year on a moon mission and in addition to those missions there are several ion engines performing on Earth satellites as station keeping thrusters.
Over a year ago I read an article about some Australian engineers and scientists who had developed a new ion thruster 10 times as efficient as the ones currently in use. Four times the thrust too.
http://en.wikipedia.org/wiki/Deep_Space_1
http://en.wikipedia.org/wiki/Hayabusa