This is a good idea:
A new computerized, scannable fare card would allow New York City Transit to charge passengers different prices depending on the time of day
Charging passengers more to ride the subway when it’s crowded and less when it’s not makes sense, just like it makes sense to charge drivers to use crowded roads. In both cases there are some transaction costs that have to be accounted for, of course — establishing a tolling system for roads and creating a variable-fare system that isn’t too complex for transit — but in both cases, price should be regulating peak demand, not the opportunity cost of time lost in traffic or the unpleasantness of jamming yourself into a thicket of strangers.
Sadly, it looks as though the MTA has ruled out charging more for peak rides, which would help relieve the overcrowding at rush hour. Even so, charging less at off-peak hours will be a net gain for the system’s riders. But why not go all the way and make the subway free when it’s not being heavily used?
Update: Charles Komanoff at Streetsblog does some great analysis of one possible variable-fare structure.