There were a lot of short line railroads in Pennsylvania that got bought up by either the Pennsylvania RR or Philadelphia & Reading Railways who later became known as the Reading Railroad in the 1920's. I try to model the Reading railroad; either Reading Lines(the freight side of Reading) or Reading Company(the passenger side of Reading). Also I have some freight cars in Reading & Northern RR from MTH.
Currently there is the Reading & Northern railroad that is operating out of an area near Allentown PA. It is a short line RR but has a lot of freight traffic between 2 major railroads(CSX & Norfolk Southern, if I am correct) in Pennsylvania and is looking to expand into passenger service near Reading & Hamburg PA. Reading & Northern also services the Prell shampoo factory near Mahopany PA.
I'm sure there are other states that had a lot of short line railroads but those are the ones I know of. I know that Georgia and North Carolina had some small railroads as well.
Lee Fritz