The main gun you'll see in the game is the Tanegashima, a Japanese matchlock arquebus. This gun is the only Japanese firearm made for the next couple of centuries and is used by the in-game Ashigaru units as well as Portuguese Missionaries.
Total War: Shogun 2 — Fall of the Samurai is an expansion pack for the game that sets it in the late 1800's and adds quite a lot of firearms to the game.
Smith & Wesson Model 2
The Smith & Wesson Model 2 is added with this expansion pack and usually seen with officers and also used by the Foreign Veteran agent during the campaign.
Most of the line infantry-type, levy infantry-type, and skirmisher-type units (with the exception of Tosa Riflemen) in Fall of the Samurai used the Pattern 1861 Enfield Musketoon. Units like the Shinsengumi, Yugekitai, and the foreign-recruited U.S. Marines use this particular model. Oddly enough, they use the same gun albeit with different ranges depending on the unit stats.
The British Snider-Enfield Rifle is used by more elite troops, usually by the Imperial/Shogunal/Republican Infantry unit, the Kihetai, and the foreign-recruited Royal Marines.