I actually have a different color pin on my "places I've visted map" for cities I've only flown through and not actually visited. Off the top of my head that includes:

CVG
BRU
COS
MIA
SJU
DTW
DFW
PHX

There are quite a few cities I've done very quick trips to such as just staying for a night where I ventured into the city for a couple of hours but the above places are places I never left the airport.