Guns were being introduced all through that war, Kaleb. It would be hard to claim one was the " most popular." And it depends on which side of the conflict you are looking. Northern units were issued with a series of rifles made in theSpringfield Armory, and by contract elsewhere. Enfields were popular in the South at the beginning of the war because they were imported. But the South was also equipped with Springfield. As the War progressed, other guns, particular repeaters, with cartridges, came into being, and were bought by individual soliders as " private arms ". That would certainly be an indication of popularity, no? Include the Spencer.52 cal. and the Winchester .44 rimfire at the end of the war in those two categories. Lots of handguns were purchased privately, too. Cartridges had come into popularity with the .22 RF in 1857, followed by .32, and .38 rimfire cartridges in small revolvers. Smith and Wesson could not keep up with the orders. These small caliber guns were used as backup by cavalry troops when their heavy revolvers were shot out, and they were at saber length with the enemy.
As for duability, the Springfield certainly has to be considered as one of the better guns, but the Enfields were no slouch, either. Nor were there many complaints about the Spencer rifles or carbines. The Winchester came into the War at the end, and did not see enough use to get a very good read on durability. However, any dent in the thin magazine tube under the barrel could stop the gun being used as a repeaters, and the model 1866 was made with both a steel receiver, a wooden forearm, and a thicker tube, whereas the earlier " Henry" was made with a brass receiver, and had no wooden grip to protect that thin tube. In revolvers, the Remington .44 was considered the stronger one of all the guns made and used, because it employed a topstrap on the frame. It was preferred to the Colt .44 revolvers. Colt heard the music, and in 1873, introduced the Peacemaker in .45 Colt cartridge, with sturdy stop strap, a beefy cylinder, and a better balance. Later that same year, The Peacemaker was chambered for the .44-40. They remain the 2 longest made centerfire cartridges in the world. Part of that is due to the guns chambered to use the cartridges.
The American Civil War was a huge labratory for developing firearms. There was a drive to use the new manufacturing capabilities to produce repeating rifles of all kinds. Lincoln actually test fired a Spencer carbine on the White House grounds, when the inventor could not get a fair hearing with the old Generals in charge of ordinance. They were screaming because of all the different caliber guns they had to provide ammunition for, and the logistics of doing that when their were no good roads, and only a few railroads, even in the North. You can't blame tham for not wanting another size cartridge to have to produce and supply troops. But, Lincoln was so impressed with both the simplicity and accuracy of the Spencer, that he sent a note to the War Department directing them to give the company an order for several thousands of them. While a few Western regiments armed themselves privately with the Winchester " Henry " rifles, in 1865, the Spencer is the only repeater ordered by the government during the war. BTW, Dr. Gatling invented his Gatling gun, but by the time some of them made it to the front lines, they were not well used, and were not critical to the winning of any battle at the end of the war. Part of the reason is that officers had been trained to use Cannon, and had no clue how to use the Gatlings effectively. The guns were often set up behind the lines with the cannons, negating their sheet of fire advantages when used in the front lines, much as a machine gun would be used today. The gatlings were finally mastered and the field tactics to use them after our CW ended, in battles in Europe, Asia, and Africa. The Gatlings were used in the Spanish American Civil War in taking the Heights over Santiago, Cuba, in 1898. But they were soon replaced with Colt's machine guns, and other John Browning designs. In fact, a few machine guns were also used in Cuba.
I am sorry this wandered a bit away from the American Civil War, but before you can decide why some guns were like, others not, and really, how to even judge "durability", you have to understand that what happened in firearms manufacturing and invention during the War is part of a long history of firearm development. What was being used in the war of 1846-48 in the battle with Mexico only spurred developments before the ACW. During the War, with all the profits being earned by the companies, new tooling was purchased, or made, and new guns were being invented and perfected to solve chronic problems of open powder, and paper cartridges, which rarely functioned very well in the rain. The advent of the closed cartridge, made first of copper, and later of brass solved many of these problems as well as allowed easier and safer transportation from factory to battle front. Copper casings were the main drawback of the repeaters used in the Civil War, because the copper swells when hot, and with any dirt in the chamber, will freeze in the chamber, and not eject. Its was this fact that was instrumental in the Fetterman Massacre in 1866 in what is now Wyoming, along with his disobeying a direct order not to go out of sight of the fort. Not wanting to blame an dead officer, the ordinance department decided to blame the copper casings, and ordered new ammo with brass casings. That lead to the death of the then " new " .50-70 cartridge to the .45-70 cartridge introduced also in 1973.
When you understand the problems that ML guns faced in battle field conditions, and then understand what industry was capable of doing at the beginning of the war, and what it achieved during the war, you can better understand why there were so many guns used in the War, and why you can start a huge argument trying to answer all your " superlative " questions. For the average soldier, the"best"gun was the one that he used to save his life. In that end, that is what all Wars come down to- survival.