A poorly rendered Glock pistol is seen with Reiko Asakura in "Teamwork".
Glock 17
A Glock 17 is seen with Yusuke Harada, son of Hakata City mayor Shotaro Harada, in "Ninth Inning, Two Outs". The reason why he has a pistol is because of his father's connections to the underworld. Nguyen uses one in "Tryouts" when he goes on a Murder Inc.-backed op to assassinate Saito. Some Kakkyuu Association 49ers use them as their sidearm.
Makarov PM
A Makarov PM with black grips is used by Naoya Nitta in "Pinch Hitter". A regular one is used by Sheung Wan Red Pole named Lau in "Brawl".
M1911A1
A M1911A1 is seen in the OP sequence, "Stray", and in the ED sequence "Dirty Bullet". One is seen near Munakata in "Teamwork", being used as his main sidearm.
Type 82-2
A Type 82-2 knife pistol is used by Lin Xianming as his main knife/sidearm in case of a close encounter, which befits his Chinese upbringing. Nguyen briefly seizes it when the train shakes for a bit that made Lin drop it before the assassin takes it and uses it to kill the Murder Inc. assassin.
Tokarev TT-33
The Tokarev TT-33 appears to be used by the KA as their sidearm with Lin taking one in the middle of "Teamwork". Feilang uses it to shoot at Banba in "Walk-Off Home Run".
Revolvers
Ruger Blackhawk
A Ruger Blackhawk is seen with Yagi, the Matsuda family butler in "Lead-off Hitter".
Submachine Guns
M1928 Thompson
The M1928 Thompson is seen with Genzo Gohda aka G.G. near the end of "Walk-Off Home Run", which was his primary weapon of choice when he was a mercenary assassin.
Assault Rifles
Type 56
The Type 56 assault rifle with no folding bayonet is seen with armed guards inside an assassin training camp in China during Lin's flashback in "Hit and Run".
Sniper Rifles
Remington M24
A Remington M24 is used by Munakata when he remembers his first encounter with the Niwaka Samurai in "Teamwork".
Grenades
Mk 2 hand grenade
A Mk 2 hand grenade is seen in "Tryouts" by Nguyen, although Lin figures out later that it's a dud.
Others
Crossbow
Feilang uses a crossbow to shoot a bolt at Banba in the middle of "Walk-Off Home Run" before it misses.