The Capitol Corridor folks spent nearly a million dollars retrofitting one of their locomotives to emit less particulate matter.
You want to really do something about diesel locomotive emissions? How about electrifying the lines? Not only would that eliminate locomotive emissions (yes, there would be power-plant emissions instead, to the extent that non-emitting power sources - like solar, wind and nuclear - don't get used to generate the power), but it would allow deployment of EMU consists that would be able accelerate much better, meaning a faster journey, making the trains more attractive for commuters.
But instead, that's a million dollars we now don't have to electrify the lines or, better yet, to start high speed rail service. Congrats!