This is the correct answer. And there are so many more!

From http://deadessays.blogspot.com/2012/11/the-grateful-dead-and-trains-guest-post.html

Casey Jones ("Driving that train, high on cocaine")

Caution (Do Not Stop On Tracks) (song title)

Childhood's End ("When I was hoppin' freights")

China Cat Sunflower ("double-E waterfall" - as in "flaggin' down the double-E")

He's Gone ("Like a steam locomotive rolling down the track")

Jack Straw ("Gotta go to Tulsa, first train we can ride")

Lazy River Road ("Bright blue box cars, train by train")

Might As Well ("Long train running from coast to coast")

New Potato Caboose (song title)

New Speedway Boogie ("This train's got to run today")

Operator ("My rider left upon the Midnight Flyer")

So Many Roads ("Thought I heard that KC whistle moaning sweet and low")

Tennessee Jed ("Listen to the whistle of the evening train")

Terrapin Station ("But the train's put its brakes on and the whistle is screaming")

They Love Each Other ("It's nothing they explain, it's like a diesel train")

Tons Of Steel ("She's more a roller-coaster than the train I used to know")

Unbroken Chain ("Ride you out on a cold railroad and nail you to a cross")