A Beretta 84/85 pistol is used by Alexander Kirk (Ulrich Thomsen) in "Dr. Adrian Shaw: Conclusion" when he warns his doctor about lying to him. It's hard to determine the type since the scene was shot in an unlit room.
Beretta 92FS
The Beretta 92FS is used by one of Kirk's men in "Dr. Adrian Shaw: Conclusion". Tony Giannusa (Alfred Sauchelli Jr.) uses it in "The Harem" (No. 102)". One of Bogdan Krilov's men is seen with it in a vision in "Dr. Bogdan Krilov (No. 29)". Rhinhart (Anthony Cochrane) uses it in "Mr. Kaplan (No. 4)".
The Glock 17 is used by Oscar (Jojo Gonzalez) when his team nabs a VIP at the start of "The Thrushes (No. 53)". Suppressed Glock 17s are used in "The Forecaseter (No. 163)". The Harem uses them in "The Harem (No. 102)". Monaco Police use them in "Isabella Stone (No. 34)" with Baz (Bazzel Baz) using them after disarming an officer with the latter using it again in "Dembe Zuma (No. 10)".
Glock 19
The Glock 19 is used by Mato (Raoul Trujillo) in "Esteban (No. 79)". Silas Gouldberry (Adam Godley) uses one near the end of "The Lindquist Concern (No. 105)". One of Kirk's men uses one with a suppressor as well as Odette (Annapurna Sriram) when attempting to execute Liz at the end of "Dr. Adrian Shaw: Conclusion". Farook al-Thani (Anthony Azizi) uses it in "The Lipet's Seafood Company (No.111)". Reddington takes one from a Monaco police officer in "Isabella Stone (No. 34)". Some FBI agents use them as their main sidearm.
Glock 26
A Glock 26 is used by Reddington to interrogate the Hunter in "Dembe Zuma (No. 10)".
Heckler & Koch HK4
A Heckler & Koch HK4 with a mounted suppressor is used by an assassin in "Miles McGrath (No. 65)". At first glance the slide appears to be stainless or have a nickel/chrome finish, however based on the fact that there are areas of the slide that retain the original blueing (most notably the safety recess and the slide serrations) it appears to be a standard slide which has had the majority of the blueing removed to show the bare metal beneath.
Makarov PM
The Makarov PM is seen in "Mato (No. 66)" by Liz and Kirk.
An Orion Flare Gun is used by Liz in "Mato (No. 66)" to fire a distress flare.
Percussion Cap Pistol
A Percussion Cap Pistol is seen hanging on the wall of an apartment room in "Mr. Kaplan (No. 4)".
Smith & Wesson M&P Shield
A Smith & Wesson M&P Shield is used by Liz as her backup sidearm after she got reinstated to the FBI. Nikolaus (Cameron Pow), one of Reddington's agents, turns on Werner von Hauser in "Dr. Bogdan Krilov (No. 29)".
SIG-Sauer P228R
What appears to be a SIG-Sauer P228R is seen in "Isabella Stone (No. 34)" with Monaco police officers before Dembe takes one.
SIG-Sauer P228
Dr. Bogdan Krilov (Rade Serbedzija) loads up what appears to be a two-tone SIG-Sauer P228 in "Dr. Bogdan Krilov (No. 29)" (S4E19).
SIG-Sauer P232
What appears to be a suppressed SIG-Sauer P232 is used by an assassin hired by Miles McGrath in "Miles McGrath (No. 65)".
Smith & Wesson 4506-1
A Smith & Wesson 4506-1 is used by a gunman in "Requiem".
Smith & Wesson SW1911 Compact ES
A Smith & Wesson SW1911 Compact ES is used by Dembe in "Dembe Zuma (No. 10)", using it as his main sidearm in the season.
Walther PPK
A Walther PPK is used by Liz in the middle of "The Harem (No. 102)".
X26 Taser
An X26 Taser is used by Ressler to subdue Natalie Luca in "Natalie Luca (No. 184)".
Revolvers
Smith & Wesson Model 10
What appears to be a Smith & Wesson Model 10 is used by a PNR officer in "Esteban (No. 79)".
Smith & Wesson Model 36
A Smith & Wesson Model 36 is used by the Architect as his sidearm in "The Architect (No. 107)".
SIG-Sauer MPXs fitted with side folding stocks are used by some of Kirk's men throughout "Dr. Adran Shaw: Conclusion". It is also seen with some of the armed men raiding an underground hacker's hideout in "The Architect (No. 107)".
Assault/Battle Rifles
Bushmaster ACR
The Bushmaster ACR is used by Royal Canadian Mounted Police Emergency Response Team operators in "Mato (No. 66)" in a raid.
PTR 32P PDW R pistols fitted with folding stocks, EOTech sights, rails and suppressors are used by Miles McGrath (Tate Ellington) and Johan Halbeck (Manny Perez) in "Miles McGrath" (No. 65), although the former only plays around with it. This rifle is also used by one of Reddington's men in "The Thrushes (No. 53)".
PTR PDW R
A PTR PDW R with a folding stock, EOTech sight, rails and mounted suppressor are used by Johan's men in "Miles McGrath" (No. 65).
SIG-Sauer 516 Tactical Patrol
SIG-Sauer 516 Tactical Patrol carbines are used by most of Reddington's forces and occasionally by FBI SWAT teams. Tom Keen uses one while leading a raid with mercenaries on Kirk's safehouse at the end of "Gaia (No. 81)".
Shotguns
Sawed-off Shotgun
A sawed-off shotgun is used by one of Mato's Cuban associates in the middle of "Esteban (No. 79)".
Sniper Rifles
AR-15 Carbine DMR
An AR-15 Carbine DMR is used in the end of "The Debt Collector (No. 46)" when he takes a shot at Reddington.
DRD Tactical Kivaari
A DRD Tactical Kivaari is used by Reddington's men in "The Debt Collector (No. 46)".
Robar SR-21
A hired assassin uses a Robar SR-21 sniper rifle to assassinate a VIP in "The Thrushes (No. 53)".
Several M7 CS Grenades are seen in "Miles McGrath (No. 65)".
M84 Stun Grenade
A M84 Stun Grenade was hurled inside an unmarked train car in "Miles McGrath (No. 65)".
Model 7290 flashbang grenade
A Model 7290 flashbang is used by the Architect to cover his escape in "The Architect (No. 107)". Another is used by Krilov's men in "Dr. Bogdan Krilov (No. 29)".
Special Weapons
Kinetic Energy Penetrator
A Kinetic Energy Penetrator is used by Aram at the end of "The Architect (No. 107)" to take out the Architect's getaway vehicle.
Others
Small Arms Arsenal
An arsenal of small arms is seen with Johan in "Miles McGrath (No. 65)".
Crossbow
A crossbow is used by the Hunter (Leon Rippy) in "Dembe Zuma (No. 10)".