Some countries actually use mass transit.  Especially countries where urban centers are as densely packed as they are in Japan.  East Japan Railway Company servers some 16 million passengers every day.  When your citizens use mass transit, it becomes important to make that transit efficient and non-polluting.  JR East is working on alternative fuels for it's train system.  We've already mentioned their hybrid train technology, but now they're taking another step with a plan to introduce a fuel cell powered train. 

Right now they're still in the planning stages, of course.  The first trial would have a one-car train pushing 65 mph and emitting only water as its waste.  The train will also be 'hybrid' in that electric batteries will also power the train and charge when the train breaks.

 

The biggest obstacle to the introduction of hydrogen vehicles has always been lack of infrastructure.  How many gas stations have you seen with hydrogen pumps?  This is less of an obstacle for trains, because there are fewer fueling stations and the fuel cell trains will follow specific lines, but creating the infrastructure will still be a challenge.