City of New Orleans - written by Steve Goodman, cover by The Highwaymen - the City of New Orleans is a passenger line still operated by Amtrak between Chicago and New Orleans

The Gallopin' Goose - C. W. McCall - not exactly a train but certainly a part of railroad history, the "Galloping Geese" were a product of the declining demand for passenger rail service:

Originally running steam locomotives on narrow gauge railways, the perpetually struggling RGS developed the first of the "geese" as a way to keep its contract to run mail into towns in the Rocky Mountains in Colorado. There was not enough passenger or cargo income to justify continuing the expensive steam train service at then-current levels, but it was believed that a downsized railway would return to profitability.
[...]
Motors were not only less expensive to operate, but were also significantly lighter, thus reducing impact on the rails and roadbeds.
[...]
The first was built in 1931 from the body of a Buick "Master Six" four-door sedan.

The Legend of John Henry's Hammer - Johnny Cash (the Folsom Prison recording) - also not about a train specifically, but about the legendary railroad steel driver John Henry, I think it fits

Orange Blossom Special - written by Ervin T. Rose, cover by Johnny Cash - the Orange Blossom Special was a passenger train running between New York and Miami

*Bonus:

Dumb Ways to Die - produced by Metro Trains Melbourne as part of a public awareness campaign for railway safety in 2012