Images
Photographs of Southern locomotives, cars, track, stations, etc are very hard to find in their Civil War and pre-Civil War configurations. I have located few such photographs and have not succeeded in getting permission to publish any. If anyone can direct me to others, I will gladly attempt to get permission to post them. Go here for the photographs I have (all from the Library of Congress).
 
Artist Jim Jordan has produced a likeness of the Western & Atlantic locomotive General in the 1862 "Great Chase"
 
Artist John Paul Strain has produced the likeness of a generic, late 1850's locomotive at "Charleston Station"
 
Alan Edwards shares this photo of the Mobile & Girard Railroad Seal
 
John Stewart, of Birmingham Rails, provides this 2006 photo of a culvert on the South & North Alabama RR. He has seen many culverts on the original Louisville & Nashville RR and says they are much like this one.
 
This is a scan of an envelope, printed for use by the Confederate Locomotive Shops in Raleigh, but mailed in Columbia, S. C. Since Capt. Thomas R. Sharp was officer in charge of the shops in Raleigh and, when they were closed, went to be the Superintendent of the Charlotte & South Carolina RR, in Columbia, it is likely that he used this envelope in Columbia. The envelope was addressed to the Superintendent of the Ordnance Works in Salisbury, N. C., who was arranging to get a lathe from the Locomotive Shops for his Works (see here and here). A second envelope is here.
 
Other scans/photographs provided by site users:
Memphis & Charleston Railroad Ticket
Mississippi & Tennessee Railroad Pass
Mobile & Ohio Railroad Locomotive William Jones Jr.
Raymond RR Spikes The shorter (5 1/2 inches long) were for strap rail; the longer (7 1/2 inches long) were for T-rail. Weight was about 8 to 9 ounces. Photo provided by William Elkins.
U-Rail Cross Section Photo of Jim Hinson collection
Virginia & Tennessee RR Cover Photo provided by Larry Baum
Wilmington & Manchester RR Baggage Tag Photo of Jim Hinson collection
Wilmington & Manchester RR Way Baggage Tag Photo of Jim Hinson collection
Wilmington & Manchester RR Lock Cover Photo of Jim Hinson collection
 
Below are some of the many pieces of Confederate, state and railroad currencies and shares of stock that had trains depicted on them or were issued by railroads companies.
$10 Confederate - front Back of same, showing post-war Atlantic & Great Western advertisement
$50 Confederate
$100 Confederate The train on this bill is also found on the $20 North Carolina note of March 1, 1862, and the $1 Georgia notes of January 1, 1863 and April 6, 1864
$100 Confederate The train on this bill was also used on the $2 Florida note of 1863-64.
$1 Georgia  Detail of the train on this bill
$10 Georgia Detail of the train on this bill
$20 Mississippi
50c Bank of Tennessee
Alabama & Tennessee River RR 25c 1862 Angelos
Alabama & Tennessee River RR Bond, due 1864 Beach
Alabama & Tennessee River RR Stock 1864 Angelos
Alexandria, Loudoun & Hampshire RR 25c 1864 Angelos -- this was issued when the road was under Union control
Central (of Georgia) RR $1 & $2 1861
Central (of Georgia) RR 15c 1861 Angelos
Clover Hill RR Stock 1864 (a branch of the Richmond & Petersburg RR) Angelos
East Tennessee & Georgia RR 1862 50c Angelos
East Texas RR Stock 1861 
Galveston, Houston & Henderson RR 1862 50c Angelos
Greenville & Columbia RR Stock 1863 Angelos
Manassas Gap RR 1861 $1  Angelos
Memphis & Charleston RR 1862 50c Angelos
Mississippi & Tennessee RR 1862 $2 According to family tradition, the locomotive is the Hugh McGehee -- Johnston
Mississippi & Tennessee RR 1862 $3 Angelos
Mississippi Central RR 1863 25c Priestly
Mississippi Central RR 1862 50c Priestly
Mississippi Central RR 1862 $1 Angelos
Mississippi Central RR Stock 1862 Angelos
Mobile & Girard RR 1862 $3 Angelos
Mobile & Ohio RR 1862 10c Angelos
Mobile & Ohio RR 1862 25c  Ellison
Mobile & Ohio RR 1862 50c Ellison
Mobile & Ohio RR 1862 $1 Ellison
Mobile & Ohio RR 1862 $2 Ellison
New Orleans, Jackson & Great Northern RR 1862 50c Priestly
New Orleans, Jackson & Great Northern RR 1861 $1.50 Angelos
New Orleans, Jackson & Great Northern RR $3 1861
Pensacola & Georgia RR Tax, 1861 Beach
Raleigh & Gaston RR Stock 1861 Dickens
Selma, Ala. Bond in support of the Alabama & Tennessee River RR Beach
South Carolina RR 1864 50c Angelos
South Western RR 1862 $5 Angelos
Southern of Mississippi RR 1862 10c Angelos
Southern of Mississippi RR 1862 $1
Southern Pacific RR Construction Bond, unissued Beach
Vicksburg, Shreveport & Texas RR 1862 50c Angelos
Virginia Central RR 1861 $20 Angelos
Virginia & Tennessee RR Stock 1861  Angelos
West Feliciana RR 1862 $2 Angelos
Western & Atlantic RR 1862 10c Angelos
Western & Atlantic RR 1862 25c
Western & Atlantic RR 1862 $1
Wilmington & Manchester RR Stock 1862 Beach
Wilmington & Manchester RR Stock 1863 Larry Baum
 
The images with "Angelos" after them are provided by Pete Angelos, whose collection can be found at webpages.charter.net/marlofan/index.html
The images with "Beach" after them are from the web site Cigar Box Labels at www.cigarboxlabels.com
The images with "Priestly" after them were provided by Bill Osborne from the collection of Seymour Priestly. Those labeled Ellison come from Stephen Ellison. Those labeled Dickens are from Jeff Dickens.
The images with "Johnston" after them were provided by Robert Johnston, whose ancestor, Francis Marion White, was President of the Mississippi & Tennessee RR during the War.