The Beretta 92FS is used in Perfect Order as Akihiko Tojo as his primary sidearm until he's told to change to the SIG SP 2022, first seen in Perfect Order's OP sequence, "UNDER/SHAFT".
Browning Hi-Power
The Browning Hi-Power is used by Jonathan "Jonah" Mar in Perfect Order as his primary sidearm until he's told to change to the SIG SP 2022, first seen in Perfect Order's ED sequence, "Ambivalentidea".
CZ 52
The CZ 52 is seen briefly in flashback sequences in "The Snake that Admires the Heavens".
Heckler & Koch Mark 23
The Heckler & Koch Mark 23 is used by Lehmbrick as his primary sidearm until he's told to change to the SIG SP 2022, first seen in Perfect Order's OP sequence, "UNDER/SHAFT".
Heckler & Koch P7
The Heckler & Koch P7 is seen with an armed man working for Spin in "The Snake that Admires the Heavens".
M1911A1
A M1911A1 is used with an armed man working for Spin in "The Snake that Admires the Heavens".
SIG-Sauer GSR
Karen Lo is seen with her SIG-Sauer GSR, briefly in flashback sequences in "The Snake that Admires the Heavens".
SIG SP 2022
The SIG SP 2022 is seen with everyone in Koko's team from "Dance with Undershaft phase.1" in an attempt to give them a common sidearm.
Smith & Wesson M945 Compact
The Smith & Wesson M945 Compact is seen briefly in flashback sequences in "The Snake that Admires the Heavens" with Dominique.
Taurus PT 24/7
The Taurus PT 24/7 is seen with Hex as her sidearm with the CIA Special Activities Division.
Assault Rifles
AKS-74U
The AKS-74U is seen briefly with Jonah in a flashforward sequence in "The Snake that Admires the Heavens" and later on "Century of Shame". Hex and her CIA Special Operations Group team in Eastern Europe use them in "Dance with Undershaft phase.1".
Colt Model 733
The Colt Model 733 is seen in Perfect Order's OP sequence, "UNDER/SHAFT".
Colt M4A1
The Colt M4A1 is seen with American military forces.
FN SCAR-L
Hex uses an FN SCAR-L as her primary assault rifle in the Czech Republic. Note that she uses Magpul PMAGs which would work poorly in the rifle until later Gen M3 PMAGs.
Magpul Masada
The Magpul Masada is used by Koko's HCLI team in an attempt to give them common small arms after it shows up in "Dance with Undershaft phase.1". It's also seen in Perfect Order's OP sequence, "UNDER/SHAFT" and in the ED sequence, "Ambivalentidea". They're usually seen with EOTech sights attached to the upper receiver. Its inclusion was based on the manga at the time when it was published in Japan from the early 2000s, the Masada was being marketed as a potential weapon for the US military before Bushmaster/Remington took over in further developing and marketing the assault rifle.
Mk 18
The Mk 18 is seen with the SOG team in an Eastern European flashback sequence in "Dance with Undershaft phase.1".
Steyr AUG
The Steyr AUG is seen with Valmet in the season before she's told to change to the Masada.
Vektor CR-21
The Vektor CR-21 is briefly seen with Eckhart aka Echo in an Eastern European flashback sequence in "Dance with Undershaft phase.1".
Sniper Rifles
Remington 700PSS
Lehm is seen firing a Remington 700PSS in Perfect Order's OP sequence, "UNDER/SHAFT". It's seen briefly in "The Snake that Admires the Heavens" when Koko explains to Jonah the CIA's paramilitary aspects.
Machine Guns
Gryazev-Shipunov GSh-301
The Gryazev-Shipunov GSh-301 is seen on a SU-37 in Perfect Order's OP sequence, "UNDER/SHAFT". In "Century of Shame", it's seen with SU-37 in service with the NUSSRAF.
Grenades
M18 smoke grenade
The M18 is seen with the SOG team in an Eastern European flashback sequence in "Dance with Undershaft phase.1".
Others
Arms Cache
A shot of AK-74-based rifles in open crates are seen briefly in "The Snake that Admires the Heavens".