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
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.
Snider-Enfield rifle
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.
Spencer repeating rifle
The American Spencer repeating rifle is used by the Tosa Riflemen and some Cavalry units.
Chassepot 1866 bolt action rifle
French Chassepot 1866 rifle is the main rifle of the game and is common to see with troops.
Gatling Gun
The Gatling Gun is also in the game, serving as a lethal weapon against cavalry units.
Armstrong gun
The standard artillery piece in the game is the Armstrong Gun.