Remember the train in Dr. Zhivago? Cold, dark, threatening. How different than our nostalgic view especially reflected in popular music. I am starting a playlist with trains as the theme.
(any thoughts as to Classical's seemingly empty references?)
My first five...please augment.
It Takes a Lot to Laugh, It takes a Train to Cry.
Garfield and Scaggs version.
China Cat Sunflower  Europe 72
The City of New Orleans Arlo Guthrie
Rose of Cimarron Poco
Take the A Train Duke Ellington (Any version suggestions?)

Arthur Honneger “Pacific 231”

Heitor Villa Lobos “The Little Train of the Caipira”

John Coltrane “Blue Train”

Andrews Sisters “Chattanooga Choo Choo”

Pat Metheny “Last Train Home”

Jeff Beck “The Train Kept A Rollin’”

Leave it to Honneger! Thanks for that. 
Holly Cole’s cover of Tom Waits Train Song.
I like the Holly Cole cover of "Train Song", but I think the live version from her "Best of" album is even better than the studio version. Check it out......

Holly Cole - "Train Song"  - Live
Adrian Belew  - "The Rail Song" from his album "Twang Bar King"

There is also a great acoustic version on his album - "The Acoustic Adrian Belew", but I couldn't find it on youtube.

The Train and the River by Jimmy Giuffre
  Play A Train Song by Robert Earl Keen
Butterfield Blues Band (self-titled) - Mystery Train
Butterfield Blues Band (East-West) - Two Trains Running
Dave Alvin (Public Domain) - Engine 143; Railroad Bill
Merle Haggard (Same Train, A Different Time) - Waitin' For A Train; Train Whistle Blues
Dick Curless (Traveling Through) - Freight Train Blues
Steve Earl & Del McCory Band (The Mountain) - Texas Eagle
Chattanooga Choo Choo (from The Essential Glenn Miller, Disc 2) (although this tune has probably been covered by others as well)

Andy Summers - Train Song (from Mysterious Barricades)

And lastly, don’t forget the train horn and tracks sound effects at the beginning and end of Barbary Coast by Weather Report (Black Market album).

Oscar Peterson Trio - Night Train
Hellbound Train --  Savoy Brown

From the 1950’s:

Howlin’ Wolf: "Smokestack Lightning". Done by many others, not anywhere as wickedly.

Elvis, Scotty, and Bill: "Mystery Train". The Band do a good version on their Moon Dog Matinee album.

The (Johnny Burnette) Rock ’n’ Roll Trio: "Train Kept A-Rollin’" (written by Tiny Bradshaw). Done by a lot of others (the first version I heard was that by The Yardbirds, Jeff Beck on guitar), but not anywhere near as hot. Aerosmith’s version sucks.

The Rock ’n’ Roll Trio: "Lonesome Train (On A Lonesome Track)". Johnny Burnette was a better Rockabilly singer than Elvis imo.

Johnny Cash: "Hey Porter" and "I Walk The Line".

Louis Jordan: "Choo Choo Ch’Boogie". Audiences love to dance to this cool Jump Blues tune. Done by many others, Asleep At The Wheel’s version a good one.

Early 1960’s: Little Eva: "The Loco-Motion" (written by Carole King & Gerry Goffin). Grand Funk Railroad’s version sucks.

Paul Revere & The Raiders: "Night Train". Done by a LOT of people, theirs being the first I heard. For the ultimate Garage version, listen to that by The Sonics. Makes The Ramones sound mellow.

Late 1960’s onward:

The Kinks: "Last Of The Steam Powered Trains", on their fantastic The Village Green Preservation Society album.

Dan Hicks & His Hot Licks: "Waiting On The 103".

Taj Mahal: "She Caught The Katy".

The Band: "Just Another Whistle Stop". Phil Lesh does a version, haven’t heard it.

Dylan: "Slow Train".

Guy Clark: "Desperados Waiting For A Train".

Crazy Horse: "Gone Dead Train".

Bill Frisell: "Gone, Just Like A Train".

Train In Vain - The Clash
Last train to Clarksville - Monkeys 🇦🇺
California Zephyr - Ben Gibbard and Jay Farrar
City Of New Orleans - Steve Goodman (who wrote it)
Peace Train - Cat Stevens
Just Like This Train - Joni Mitchell
Train In The Distance - Paul Simon
Johnny Cash

”I’ve Got A Thing About Trains”

“I Hear That Train A Comin”

”All Aboard The Blue Train”

“Locomotive Man”

“Let The Train Blow The Wistle”
Does Jethro Tull's Locomotive Breath qualify?

Steve Earle album Tran A Comin' has a song Mistery Train part II
"Long train running" - Doobie Brothers
Orange Blossom Special
(too many great versions to choose)
Station Man  Fleetwood Mac
John Hammond   Wicked Grin
Bruce Cockburn   Night Train
Downtown Train - Rod Stewart

Morning Train - Sheena Easton

I will redeem myself for that last one with this one:

Crazy Train - Ozzy Osbourne

Nice list;

+1 Bruce Cockburn - Night Train

And I’ll add;

Lynyrd Skynyrd - Railroad Song

Tom Petty - Runaway Trains

John Prine - "Morning Train"

From the fantastic JP album - "Fair and Square"
Can’t believe I forgot Aerosmith’s cover of Train Kept A Rollin’ and Hendrix Hear My Train A Comin’
Here's 2 oldies 
Rock Island Line
Midnight Special
"Last Steam Engine Train" by both John Fahey and Leo Kottke
Train To Nowhere · Eric Clapton · Mark Knopfler · Don White

JJ Cale "Lonesome Train"

J.J Cale  Ridin' Home

Charlie McCoy (playing harp on that song above too)
I heard that lonesome whistle

J.J. Cale  End of the line

Ray Bryant Slow Freight

Ray Bryant  Lonesome Traveler

William Elliot Whitmore "she had a fear of trains"
@roberttdid Downtown Train was written and originally performed by Tom Waits. Personally much prefer his version to Rod Stewart's.

Steve Reich, Different Trains
Jill Sobule Trains
"Midnight Train to Georgia" Gladys Night & The Pips
Does the band Train count?
Robert Earl Keen - "Lynnville Train".
(cover) Dawn McCarthy & Bonnie 'Prince' Billy- "Milk Train". 
(cover) 2:19 - John Hammond.
"Midnight Flyer" - The Eagles

"Tennessee Central No. 9" - Roy Acuff

Joachim Cooder - "When the Train Comes Along".
"The Railroad" Grand Funk Railroad

Do I get dbl points?
Pete Droge - "Northern Bound Train"
Passage to Bangkok- Rush