I've added MTA logos to my Flushing 7 World's Fair set, as well as added some passengers to many of my sets. But mostly I just run them and enjoy the heck out of them.
I run a temporary layout on banquet tables (a 4 x 8 Mianne is coming, but even then Ill run it as a blank slate so I can frequently change it.) I'm not a modeler or scale guy, I'm a toy train guy, and frequently create fantasy layouts.
I say this because the most current layout will feature some Plasticville, but also a collection of actual NY World's Fair memorabilia that I have. Oh--and subway maps make a great surface for setting up my subway layouts.
Enjoy these subway sets. I really hope somebody keeps making them!