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The Borchardt C-93 is seen as the main sidearm of Lieutenant Tsurumi in the show.
Colt Model 1903
The Colt Model 1903 is seen in "Grim Reaper" during an imagine spot.
Mauser C96
The Mauser C96 is seen in "Race" in an arms stash.
Revolvers
Type 26 Revolver
The Type 26 Revolver is seen with an armed man in "Nopperabo" before Sugimoto takes it. It's also used by soldiers/officers of the 7th Infantry Division and by Tatsūma Ushiyama in "Kamuy Mosir", being their sidearm. Other characters use it from time to time.
Battle Rifles
Arisaka Type 30
The Arisaka Type 30 is seen with Imperial Japanese Army soldiers throughout the anime, among them including Saichi Sugimoto aka "Immortal Sugimoto" and soldiers of the 7th Infantry Division. Some Imperial Police Bureau officers use them seemingly. The Type 30 is seen in an imagine spot in "Grim Reaper" and in an arms stash in "Race".
The Mosin Nagant M1891 is seen with Imperial Russian Army forces during the Siege of Port Arthur in "Wenkamuy". At least one M1891 is seen in an arms stash in "Race".
Murata Rifle
The Murata Rifle is seen with hunter Nihei Tetsuzou in "Race", using it as his main weapon.
Winchester Model 1892
The Winchester Model 1892 is seen in "Race" in an arms stash secured by Hijikata, which he uses it as his main weapon.
The Maxim 1895 is seen with IRA forces during the Siege of Port Arthur in "Wenkamuy".
Unknown Machine Guns
The two unknown machine guns is seen in "Grim Reaper" during an imagine spot.
Others
Bow
An Ainu-made bow is used throughout the anime by Asirpa aka Asuko Kochuobe, an Ainu girl from Hokkaido as her main weapon. Other Ainus use it from time to time.
Bow Trap
A bow trap, consisting of a poisoned arrow known as Amappo is seen in "Grim Reaper".
28 cm Howitzer L/10
Several 28 cm Howitzers are used by the Imperial Japanese Army in "Wenkamuy" during the Siege of Port Arthur.