Before the war...there is no dominent "brand" although a few large makers like Leman produced enough arms so that they had standard products and these were easily recognized. Huge numbers of ex-military muskets, used with shot and round ball, were in regular use - likely far more than rifles. All muskets made before the adoption of the Standard Model of 1815 were condemmed and sold well before the Civil War which flooded the market with well made, inexpensive guns. Virtually no shotguns were made in America, this market was compeletly dominated by Birmingham, England export guns. Also, military rifles and muskets that did not pass inspection found a ready market with western emigrants. Some makers like Robbins & Lawrence made more money on their rejected arms than they did on the accepted ones.
From the archeological evidence it appears that most Texans were still using flintlocks (understandable as Texas was at the far end of the supply chain for percussion caps) and lots of ex-British Army late pattern "Brown Bess" muskets were in use. The Mexican army was largely armed with these but the Texans used them also.
After the war...we have a wildly distorted "movie-view" of the first twenty years after the war. There is a new book coming out in the next few months titled "Arming the West". Its the shipping records of Schuyler, Hartley & Graham to their western distributors from around 1866 to 1888. By far the most popular gun sold was the M1842 musket, usually bored smooth if it had been rifled. Other muskets follow, along with many different types of surplus muzzle loaders. Single shots are next, usually M1866 .50-70 rifles, either in original configuration or shortened, but there are numerous other single shots that are also listed. All repeaters are very low down on the list. They were expensive to buy and to shoot and fragile in the bargain. The people who bought them were apparently those with a definate need for a repeater and/or the extra money to spend on a "new fangled" rifle. Lots of Sharps business rifles went to the buffalo hunting areas but single shot Allin-type breechloaders still predominated. Very few handguns figure in the list and nearly all of them percussion. (However, SH&G were close to the Remington firm which they eventually took control of so the lack of Colts is not surprising. Nevertheless, there are very few Remingtons listed as well and these would have been readily available to them).
You've asked a very good question...one that has received very little real research. I'm afraid that most gun collectors base their assumptions on movies/television and/or what they personally like.
Joe Puleo