This list include very varied financial entities. From completely defunct companies, to operating companies with operations turned into investments, some hanging onto a corporate skeleton owning properties as holding companies, or have assigned their properties in mergers, bankruptcy or other legal acts (dissolution of the corporation) and finally others having become extinct—their works either torn up and hopefully recycled, or sold off to operating companies. This list does not indicate which is which.  

The Baltimore and Ohio Railroad (reporting mark BO) was the first common carrier railroad and the oldest railroad in the United States with its first section opening in 1830. Merchants from Baltimore, which had benefited to some extent from the construction of the National Road early in the century, wanted to do business with settlers crossing the Appalachian Mountains.

The Boston and Maine Railroad was chartered in New Hampshire on June 27, 1835, and the Maine, New Hampshire and Massachusetts Railroad was incorporated March 12, 1839, in Maine, both companies continuing the proposed line to South Berwick, Maine. The railroad opened in 1840 to Exeter, New Hampshire, and on January 1, 1842, the two companies merged with the Boston and Portland to form a new Boston and Maine Railroad.

Wikipedia

The Butte, Anaconda and Pacific Railway (reporting mark BAP) is a short line railroad in the U.S. state of Montana.

Sam apparently held stock in the Chicago and Alton Railroad.  He reports in a letter to Livy "The Chicago & Alton paid a dividend of $200 July 2d—it is in Mr. Rogers’s hands. "  as reported in Day By Day for August 2, 1901.

 

The Chicago and North Western Railway was chartered on June 7, 1859, five days after it purchased the assets of the bankrupt Chicago, St. Paul and Fond du Lac Railroad. On February 15, 1865, it merged with the Galena and Chicago Union Railroad, which had been chartered on January 16, 1836. Since the Galena & Chicago Union started operating in December 1848, and the Fond du Lac railroad started in March 1855, the Galena and Chicago Union Railroad is considered to be the origin of the North Western railroad system.

The Aurora Branch, the earliest predecessor of the Chicago, Burlington and Quincy, changed its name to the Chicago and Aurora Railroad in June 1852,[8] and to Chicago, Burlington, and Quincy Railroad in 1856, and shortly reached its two other namesake cities, Burlington, Iowa, and Quincy, Illinois.

The Cincinnati, Hamilton and Dayton Railway (CH&D) was a railroad based in the U.S. state of Ohio that existed between its incorporation on March 2, 1846, and its acquisition by the Baltimore and Ohio Railroad in December 1917.

The railroad was formed on June 30, 1889 by the merger of the Cleveland, Columbus, Cincinnati and Indianapolis Railway, the Cincinnati, Indianapolis, St. Louis and Chicago Railway and the Indianapolis and St. Louis Railway.

The Cumberland Valley Railroad (reporting mark CVRR)[1] was an early railroad in Pennsylvania, United States, originally chartered in 1831 to connect with Pennsylvania's Main Line of Public Works.

The Delaware and Hudson Railway (D&H) (reporting mark DH) is a railroad that operates in the Northeastern United States. In 1991, after more than 150 years as an independent railroad, the D&H was purchased by the Canadian Pacific Railway (CP).

see section from 1895 journey from Elmira to Cleveland

The Railroad Comes to Town (1867)   The Utica, Chenango and Susuehanna Valley Railroad reaches Waterville from Utica, November of 1867.  Later to be DL&W, Utica Branch

History of Chenango and Madison Counties, New York
By James Smith, 1880, Page 96

The Detroit, Grand Haven and Milwaukee Railway is a defunct railroad which operated in the US state of Michigan during the late 19th and early 20th centuries. Itself the product of several consolidations in the 1870s, it became part of the Grand Trunk Western Railroad in 1928.

Erie Railway: 1861–1878[edit]

In August 1859, the company went into receivership due to inability to make payments on the debts incurred for the large costs of building, and, on June 25, 1861, it was reorganized as the Erie Railway.

The Grand Rapids and Indiana Railroad at its height provided passenger and freight railroad services between Cincinnati, Ohio, and the Straits of Mackinac in MichiganUSA. The company was formed on January 18, 1854.

The company was incorporated on November 10, 1852, as the Grand Trunk Railway Company of Canada to build a railway line between Montreal and Toronto.[2]

Grand Trunk Western began as a route for the Grand Trunk Railway (GTR) to link its line to Chicago through lower Michigan.

The railroad first reached Decatur in 1854, when the Great Western Railroad built a line through the city. Decatur built Union Station, its first railway station, in 1856 to serve this line. By 1901, the Great Western Railroad had consolidated into the Wabash Railroad, and the old Union Station had fallen into disrepair. 

Wikipedia

The Illinois Central Railroad (reporting mark IC), sometimes called the Main Line of Mid-America, was a railroad in the central United States, with its primary routes connecting Chicago, Illinois, with New Orleans, Louisiana, and Mobile, Alabama. A line also connected Chicago with Sioux City, Iowa (1870).

When coal was discovered in the vicinity of Eldora the problem of cheap transportation became of paramount importance. This led to the formation of the Eldora Railroad and Coal Company on February 7, 1866, to build a railway to Ackley, sixteen miles north. At Ackley the Eldora road would connect with the east-west road which is now the Illinois Central. By July, 1868, the new road was completed, but its connection with the outside world was not entirely satisfactory.

In October 1867, the Cleveland, Painesville and Ashtabula Railroad leased the Cleveland and Toledo Railroad. The CP&A changed its name to the Lake Shore Railway on March 31, 1868, and on February 11, 1869, the Lake Shore absorbed the Cleveland and Toledo. On April 6 the Michigan Southern and Northern Indiana Railroad and Lake Shore merged to form the Lake Shore and Michigan Southern Railway, which absorbed the Buffalo and Erie Railroad on June 22, giving one company the whole route from Buffalo to Chicago.