Below are various bits of interesting Confederate railroad history. As I find more information about them, some may become Essays in their own right.
* William Shepperd Ashe was the first Confederate railroad coordinator. He was given the duty of coordinating the rail transportation to the armies in Virginia on July 17, 1861. There is almost nothing in the surviving record of his activities in that duty. He died on September 14, 1862 when the hand car on which he was riding was run down by a freight train. He was President of the Wilmington & Weldon RR at the time and was on his own road when the accident occurred. NP, RR 9-17-62
* The Union modified and built dozens of cars to carry the wounded from the hospitals near the army to those hospitals farther away so that the burden of caring for the many thousands of ill and wounded was spread over much of the country. Though the Confederacy eventually created a system of spreading the ill and wounded through some of the country, I have been able to find references to only six ambulance cars. Considering the shortage of cars on Southern roads and the diary entries of witnesses and soldiers, it is unlikely that there were many more than the ones located thus far.
* Very few Southern railroads ran trains at night before the war. There was little demand for night passenger service (though it was growing), the locomotive lanterns were not strong enough to illuminate the track far enough ahead of the train to make night travel particularly safe, and the people in the countryside did not want to be disturbed by trains at night. During the war, there were many instances of night rail travel for troops, passengers, and goods. The deterioration of the track made night travel much more dangerous during the war.
* Night travel was just like day travel for the passengers -- sitting upright on crowded bench seats. There were only about a dozen sleeper cars in the entire South when the war started (most on the Memphis & Charleston RR).
* For Southern railroads, Sunday running was infrequent, but not unheard of, at the war's start. War's demand caused most roads to run Sunday service for at least through freight trains.
* Many annual reports mention the damage done to box cars while transporting troops and the cost and need to repair the cars. Though some damage was probably malicious, most of it was soldiers removing boards in order to get ventilation to relieve the oppressive heat in the cars. More than a few boards were also removed so the soldiers could see the countryside as they traveled, relieving the boredom of the trips.
* On the Annual Reports to Stockholders page are listed the Fiscal Year End dates for each road. Why were the dates chosen? They bounce all over the calendar. Some dates were chosen to allow the collecting of data that had to be reported to the state on a certain date (see the Virginia and Louisiana railroads). For those roads without state reporting requirements, the date chosen was usually near the anniversary of the formation of the company. 
* Locomotives before the war were brightly and lavishly painted. Some included landscapes on the sides of their tenders. During the war, there was little time and few men to devote to keeping up the paint jobs. The colors must have faded through neglect, but the inventory of the Confederate Locomotive Shop when it closed down (NA, RRB 2-20-63) showed a good stock of all the required paint pigments. Maybe the locomotives were better painted than we suppose -- at least until 1864.
* The New Orleans, Jackson & Great Northern RR had 7 locomotives and 11 passenger cars, that had never been used, in storage when the war started -- why? This amounted to about $250,000 of rolling stock not in service. Had they been bought with the idea they would be needed if there was a war? No -- they had been bought by the previous President and Board of Directors; the new holders of those offices when the war started had been engaged in an effort to return the rolling stock to the Northern builders in order to get out from under the debt their purchase had laid on the company. They were unsuccessful; the rolling stock was used by the South and ravaged by the war, and the company still had to pay for the equipment after the war was over.
* Port Hudson, Louisiana received an unusual bit of support from the Clinton & Port Hudson RR during the siege of that place in 1863. Union cannon fire destroyed the mill that was grinding the garrison's corn. The replacement was one of the railroad's locomotives, attached to the milling machine. 
* During the Seven Days Campaign in 1862, Union troops mention hearing the whistles of the arriving Confederate trains, but note the lack of locomotive bells ringing. It was supposed that the bells had been removed to make cannon. While bells throughout the South were sacrificed to metal drives, Tredegar Iron Works was not happy with the cannon made from bell metal since it was more brittle than that normally used for cannon (it contained less tin). I have seen nothing in the documents to indicate the wholesale removal of bells from locomotives to support the war effort.
* Average train speed throughout the South before the war was about 15 miles an hour. This speed was the time from start of the day's trip to its end and includes the time spent in stations. Since stress on iron rails was dependent on the weight of the load and the speed with which it passed over the rails, the railroads universally reduced their running speeds to reduce rail wear, once they saw the war would not be over in the summer of 1861. By the last year of war, the speeds were also slower because the locomotives had been denied the maintenance they required and so could no longer pull the required weight at previous speeds. There are many stories of trains being unable to top hills because of weak, wheezing locomotives and trains traveling only slightly faster than a man could walk. 
* Besides keeping the main lines in repair, rails were eagerly sought for other needs. First, from the railroads' point of view, was the extension of sidings to handle the longer trains and the creation of new sidings to service the armies and the newly created war factories. Others wanted rails to improve the resistance of shore batteries to fire from Union warships. The Navy Department wanted rails to armor its Virginia-style ironclads (ORN Vol. 8, Page 849) -- either as rolled plates (CSS Tennessee and most other ironclads) or in the rail form (CSS Arkansas). The demand for iron of all types was so great that a government bureau was formed to seize and allocate iron (OR Series 4, Vol. 2, Page 365).
* The Piedmont RR had an interesting problem filling its Treasurer position in 1863. When the year started, James R. Callum had held the position from before the company was organized. At a winter meeting of the Board of Directors, one Director got a motion passed creating the procedures to be used if something happened to the Treasurer. According to the minutes book from that meeting, as soon as the motion was passed, word was received in the room that the Treasurer had just had a bad fall and was unconscious. One week later, at a called meeting of the Directors, it was announced that Mr. Callum had died. E. B. Meade was immediately elected to the position. Two months later, the minutes report that Mr. Meade had resigned and William M. Eldridge was elected to fill the position. Three months later, Mr. Eldridge also resigned and Henry M. Williamson was elected to the position -- 4 Treasurers in one year.  (In a day when companies normally did nothing financial upon the departure of an employee, the Piedmont was unusual in electing to pay the rest of the month's wage, for the month in which he died, to Mr. Callum's widow and child.)
* Allan Macfarlan, President of the little (40-mile long) Cheraw & Darlington RR spent December 1862 in London. His personal records show that he cashed a L1,000 check, made out to himself, on December 22 and again on December 31. Both were drawn on Aiken Roger &  Co, Glasgow. What was he doing in London and what was he buying? Since his little railroad could hardly have afforded, or needed, to send him to buy supplies just for itself, I assume that he probably bought supplies for his own road and for several others in South Carolina. The wartime records of the South Carolina railroads are particularly sparse, but we do know that the  South Carolina RR received imports in early 1863 -- perhaps purchased by Mr. Macfarlan.
* Sewall L. Fremont, Superintendent of the Wilmington & Weldon RR before and during the War spent the first six months of the war as an Engineer in the Confederate Army. One of his duties was as commander of the Cape Fear (Wilmington) region of North Carolina. He planned and constructed extensive works on Federal Point and named them Fort Fisher, after his friend, Charles F. Fisher, who had died at the Battle of First Manassas, June 21, 1861. Charles Fisher had been the President of the North Carolina RR until he raised a regiment and went to Virginia. Fort Fisher became the most powerful fort in the South, protecting Wilmington and its extensive and vital blockade running system.
* The Clinton & Port Hudson RR was so old and poorly maintained that it was said to run a tri-weekly schedule -- one week it would go down to Port Hudson and the next week it would try weakly to get back.
* On May 12, 1864 General Kautz began a second cavalry raid against the railroads between Richmond and the North Carolina border as part of Butler's Bermuda Hundred campaign. Late in the afternoon of the 13th, Kautz's troops captured Chula Station on the Richmond & Danville RR. Unable to destroy the nearby bridge, the troopers set the siding switch so that a train returning from Richmond would derail. Shortly after dark, they got their wish as a locomotive hit the switch and derailed. On the locomotive were Charles Talcott (Superintendent of that railroad) and J. L. Morrow (Superintendent of the telegraph company). The two men had been reconstructing the damage the Union raiders had done closer to Richmond for most of the day (at Coalfield and Powhatan Stations) and were heading south to repair the next batch of damage. Due to the darkness, both men and the locomotive crew were able to get away from the derailed locomotive without capture. They made their way to the bridge over Flat Creek and warned the two infantry companies there of the likely attack by the Union cavalry. Indeed, the bridge was held the next day in a small battle, much because of the warning that Talcott had given the defenders.
* From Scharf, History of the Confederate States Navy, p. 728: "To a Confederate officer, Lieut. James Barry, who had served both afloat and ashore, was due the invention and construction of an iron-clad railway battery. He and some of his men, members of the Norfolk United artillery, had served on the Virginia in Hampton Roads; and when the Confederate army was drawn behind the railroad lines around Richmond he conceived the project of, as the Richmond newspapers styled it, the "Dry Land Merrimac." Upon a double set of car-trucks he built a firm floor, upon which he erected an armor-plated casemate similar to that of the Confederate iron-clads, and mounted in it one of the Brooke banded and rifled guns so admirably adapted to firing either shot or shell. It was on several occasions brought into action on the {Richmond &} York River railroad in the neighborhood of Fair Oaks and Savage's Station, and did commendable service as long as the enemy were on the line of the road. Railway batteries are now {1887} a part of the equipment of all armies, but it is probable that the one built by Lieut. Barry was the first to go into actual service."
* It is probable that the Stevens' Battery (the ironclad battery at Morris Island in Charleston harbor) that participated in the April, 1861 bombardment of Fort Sumter was covered with some of the rails later used to lay the Milledgeville RR. NP, RD 10-12A-61
* The Atlantic & North Carolina RR locomotive "John Stanly" was painted and decorated by Samuel Hunter, a former ship's carpenter who was an amateur painter. The Raleigh Confederate of 1/6/65 says that "the work is really very creditable to Mr. Hunter's skill." Sorry, I have no idea the colors he used or the design.
* Missing luggage is not a new problem for travelers. The Wilmington & Manchester RR listed 88 unclaimed pieces of luggage in its Wilmington depot on May 1, 1863. Most pieces were trunks. Today's travelers try to make their bags stand out with bright colors or pieces of ribbon -- these pieces of luggage were mostly black, but many were red, yellow or green.
* A Company of boys, about 40 strong, was formed at Columbus, Ga. to guard the bridge at West Point, Ga. Their Captain was Walter Gordon, a brother of Major General Gordon. Not a member of the company was over 16 years old.
* Three Confederate railroads were founded by McGehee brothers. Edward McGehee (Edward) founded the West Feliciana RR, Hugh McGehee (Hugh) was a major stockholder in the Mississippi & Tennessee RR (which named a locomotive after him) and Abner McGehee (Abner) founded the Montgomery & West Point RR (which named a locomotive after him). (Information and photos provided by Robert Johnston.)
* Fletcher H. Talley was General Agent for the Memphis & Charleston RR at Memphis at the beginning of the War. Upon the capture of the city in 1862, he enlisted in Company A, Seventh Tennessee Cavalry and served until detailed for railroad service at Meridian, Miss., as agent. Upon the capture of Meridian by Sherman, he moved his office to Selma, Ala., where he continued until the capture of that place by General Wilson. After the War, he was again employed by the Memphis & Charleston RR, as General Freight and Ticket Agent. (J. Harvey Mathes, Old Guard in Gray, p. 284.
* The Conductor of the Southern Pacific RR train was named "Goodspeed."
* In late November 1864, the Hungry Hospital on the north side of Richmond asked the Engineer Bureau for 1 1/4 miles of RR iron to be used for hauling wood to the hospital. The Bureau forwarded the request to the Quartermaster's Department and received the answer that a road of wood stringers would work adequately.