A Browning Hi-Power with a suppressor is seen in the OP sequence, "Sekai wa Anata no Iro ni Naru".
Glock 17
A Glock 17 appears to be seen in an eyecatch in "The Scarlet Pursuit". Shuichi Akai aka in "The Scarlet Truth".
Heckler & Koch P7M8
The Heckler & Koch P7M8 is the personal sidearm of National Police Agency Security Bureau (NPA SB) officer Rei Furuya aka Black Organization Agent Bourbon aka Toru Amuro.
Heckler & Koch USP
A Heckler & Koch USP appears to be seen with Kogoro Mori in the ED sequence, "Unmei no Roulette Mawashite".
Heckler & Koch USP Compact
A Heckler & Koch USP Compact appears to be used in "The Dreaming Girl's Confused Deduction" by a masked man, who turns out to be Takashi Kiyose.
M1911A1
A M1911A1 is seen with Hidemi Hondou aka Rena Mizunashi aka Kir in flashback sequences throughout "The Scarlet Intersection". One is seen in an action sequence with Nagano Police Inspector Shigeru Takeda in "The Darkness of the Prefectural Police (Part 1)". The pistol is seen in is seen in the OP sequence, "Sekai wa Anata no Iro ni Naru".
Tokarev TT-33
The Tokarev TT-33 is seen in "Bodyguard Kogoro Mori" with Arimasa Dobashi. A loaded TT-33 is seen in an evidence photo in in "The Darkness of the Prefectural Police (Part 1)" and in "The Darkness of the Prefectural Police (Part 3)".
Walther PPK
The stainless Walther PPK is used by Vermouth as her personal sidearm. It's also seen in the OP sequence, "Sekai wa Anata no Iro ni Naru".
Revolvers
Nambu Model 60
The Nambu Model 60 is seen with officers of the Tokyo Metropolitan Police. Rogue Nagano Prefectural Police officer Sergeant Shinsuke Akiyama aka Shinsuka Aburakawa seizes one from corrupt NPP officer Inspector Mamoru Saegusa in in "The Darkness of the Prefectural Police (Part 3)". It's also seen in the in the OP sequences, "WE GO" and "Sekai wa Anata no Iro ni Naru".
Smith & Wesson Model 36
Smith & Wesson Model 36s appear to be seen with plainclothes officers from the National Police Agency Security Bureau (NPA SB) in "The Scarlet Truth". It's seen in the OP sequence, "Sekai wa Anata no Iro ni Naru".
Shotguns
Over and Under Shotgun
An Over and Under Shotgun is used by Danny's waiter Yasuo Nashimoto at the end of "Detective Takagi on the Run in Handcuffs".
Remington Model 870
A Remington Model 870 is seen with Akai in flashback sequences througout "The Scarlet Intersection", which has a pistol grip and short barrel.