A while ago I was visiting a buddy who is a TA at the physics department for a state university, and I was stunned to see an Apple //e hooked to a data-collection setup. It was for some kinematics experiment, for an introductory-level class.
Wasn't his idea or anything - many of the experimental setups were inherited from previous staff, and simply left as-is unless something broke. I did some digging later on, and apparently the //e was shipped as the standard interface for certain models of mass spectrometers, some (many?) of which are still in use, //e and all!
Where have you run into Apple II systems that are still in active, productive use? Amazingly, they seem to retain slivers of the foothold they once had in education. I wouldn't be surprised if there were some less-than-spectacularly-financed schools still using IIGS's and ImageWriters to print out banners.