are you going to include commuter lines?
Chicago & Eastern Illinois (C&EI)
San Pedro & Southwestern (Arizona)
El Paso and Southwestern
Arizona Eastern
Arizona & California
Magma Arizona Railway
Copper Basin Railway (Arizona)
San Manuel Arizona Railroad
The Apache Railroad (Arizona)
Central Oregon & Pacific
The Amador Central
Central California Traction
Santa Maria Valley
Modesto & Empire Traction
Sacramento Southern (A museum line, but it does have one customer)
Portland Terminal
Spokane International
State Belt Railroad
Alameda Belt
Pacific Coast
South Pacific Coast
St Luis Southwestern
Cleveland Terminal
San Diego & Arizona Eastern
Conrail
Incidently California Zephyr is the name of a train, not a railroad.
u also have a few private-owner roadnames, like Nestle or ADM (Archer Daniels Midland, a feed company) Also, most of the “fallen flags” make up today’s systems, so
Burlngton Northern Santa Fe(BNSF)- Chicago, Burlington & Quincy ( Burlington Route), Great Northern, Northern Pacific, Atchison, Topeka & Santa Fe (Santa Fe), St. Louis-San Francisco (Frisco), and Spokane, Portland & Seattle
CSX Transportation-Seaboard Coast Line (Atlantic Coast Line, Seaboard Air Line merger), Chessie System (Chesapeake & Ohio, Western Maryland, and Baltimore & Ohio merger), Louisville & Nashville, Nashville, Chattanooga & St. Louis, and Richmond, Potomac & Fredericksburg
Canadian National- (American lines only) Wisconsin Central (old Soo Line trackage), Delaware & Hudson, Duluth, Missabe & Iron Range, Illinois Cental, Gulf, Mobile & Ohio, Besssemer & Lake Erie, Grand Trunk, Vermont Railway,and Grand Trunk Western
Canadian Pacific- (American lines only) Soo Line, and Duluth, South Shore & Atlantic
Norfolk Southern- Southern Railway, old Norfolk & Southern, Norfolk & Western, Virginian Ry., Central of Georgia, Interstate RR, Wabash, and Nickel Plate Road
Conrail- New York Central, Pennsylvania RR, New Haven RR, Central RR of New Jersey, Leheigh Valley RR, Leheigh & New England, Lackawanna RR, Erie RR, and Leheigh & Hudson River. This system was bought and split up in the 1990s by CSX and Norfolk Southern.
Union Pacific- Southern Pacific, Western Pacific, Chicago & Northwestern, Minneapolis & ST. Louis, Chicago Great Western (abandoned), Missouri Pacific, Missouri-Kansas-Texas, Texas & Pacific, Denver & Rio Grande Western, and parts of the Rock Island
Guilford RR- Maine Central and Boston & Maine
Finger Lakes Rail Road
Tri Rail…a So Fla Commuter
Adirondack Railway
One old -Grand Rapids & Indiana
One new -Grand Rapids Eastern
Coopersville & Marne
Central Michigan
nuther old one- Michigan Northern
Oh, here’s one we missed: Indiana Harbor Belt .
Wheeling and Lake Erie
Akron And Barberton Belt
Akron Canton and Youngstown
Here’s a couple shortlines that either are or were around my area.
Andy
Here’s some South Dakota roadnames:
Dakota Minnesota & Eastern
D & I
Sisseton-Milbank
Ellis & Eastern
Red River Valley & Western
Dakota Southern
SunFlour Railroad
Go to the following website for info on these lines:
Here’s a couple more. One old and one brand new:
Quincy,Omaha & Kansas City (The “OK”)
Chillicothe & Brunswick (local shortline)
Palatine, Lake Zurich and Wauconda
Head-On Collision Line (yes, there really was such a railroad-it leased tank cars)
Chicago, Madison and Northern
Gulf, Mobile and Northern
Mobile and Ohio
New Orleans-Great Northern
Wilamette &Pacific
Chicago South Shore & South Bend
Chicago North Shore & Milwaukee
Pacific Electric
Chicago Milwaukee St. Paul & Pacific
Portland& Western
Mt Hood Ry.
City of Prineville
Yreka Western
Trona Ry.
Niagra Jct.
Canadian Roads,
British Colombia Ry.
Ontario Northland
Quebec North Shore & Labrador
And some Mexican roads:
Sonora,Baja California
Ferrocarril Pacifico
Nacional De Mexico
Chihuahua al Pacifico
Since someone beat me to Maine Central, and Wiscasset Waterville & Farmington, Here’s one you may not have heard of : Safe Handling Rail Inc.
old one- Litchfield, Carrollton & Western
old one still around- Peoria & Pekin Union
And one NO ONE BUT ME has heard of: Eastern Michigan & Great Lakes (a free-lanced line I thought up of until I realized it was pretty much the Wabash RR.)
Here’s some old Colorado roads
Denver, South Park, & Pacific
Colorado & Southern
Pueblo & Arkansas Valley
Denver, Leadville & Gunnison
Florence & Cripple Creek
Union Pacific, Denver & Gulf
Colorado Midland
Denver & Salt Lake
Denver & South Park
Denver & New Orleans
Denver, Leadville & Alma
Denver, Georgetown & Utah
Thanks all. The list has grown to 239 roadnames so far. Keep them coming 
Specify a date/time/era for the list. Here today, gone tomorrow.
Date/Time/Era doesn’t matter. As long as it’s US or Canada and a real railroad.
Alaska Railroad,Atlanta&West Point,Atlanta& St.Andrews Bay,Apachicola Northern,Akron Barberton Belt. Joe G.
TRRA – Terminal Rail Road Association – ran in the St. Louis, MO area as an amalgamation of rail lines to service industries. May still be the switching line in and around St. Louis. Most large cities have these switching lines that are jointly owned by the various railroads that enter the area.