The Beretta 92FS is used in Perfect Order as Akihiko Tojo as his primary sidearm 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 P226R
The SIG-Sauer P226R is seen in "Dance with Undershaft phase.2" with one of Hex's SOG operators. Kaspar's team use P226Rs, first seen while on an op in Jakarta in "Kaspar and Jonah".
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.
Submachine Guns
FN P90 TR
The FN P90 TR is seen with Kaspar's team in a flashback sequence in "Kaspar and Jonah".
Ingram MAC-11
An Ingram MAC-11 with a suppressor is used by SR operator Kaburagi at Tokyo Bay Aqua Line's Umihotaru in "Castle of Lies phase.2".
Assault Rifles
AK-47
The AK-47 is seen with some characters in some episodes.
AKM
An AKM is seen with Jonah in a flashback sequence in "Kaspar and Jonah".
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 M16A2
The Colt M16A2 is seen in in "Dance with Undershaft phase.1" in a flashback sequence with the 3rd Special Operations Group, Wide Range Communications Platoon.
Colt M4A1
The Colt M4A1 is seen with American military forces. The Special Research Unit uses it for their assault teams.
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". They're also used by Hex's SOG team in "Dance with Undershaft phase.2".
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".
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.
M61 Vulcan
The M61 Vulcan is seen mounted on a F-22 in a flashback sequence in "Kaspar and Jonah".
M249 SAW
A M249 SAW with a short barrel is used in "Dance with Undershaft phase.2" to provide fire support to extract R.
Sniper Rifles
Blaser R93 LRS2
The Blaser R93 LRS2 is seen with Lutz when working as a sniper.
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.
Grenades
M18 smoke grenade
The M18 smoke grenade 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".