In Season 4's "Faking It", retired NIS (Naval Investigative Service, the immediate predecessor to NCIS) Agent Mike Franks (Muse Watson) holds a two-tone SIG-Sauer P229 on arms dealer Arkady Kobach - in Franks' own words, a "scary S.O.B." that kept him awake for 15 years.
Beretta 92FS
The Beretta 92FS (used in lieu of the Beretta M9) appears as the issued sidearm of various military personnel and in the hands of various characters throughout the series. Gibbs uses a Beretta in his return to NCIS in "Shalom" (S4E01). Lt. Colonel Hollis Mann (Susanna Thompson) of the US Army's CID (Criminal Investigation Division) is seen carrying a Beretta 92FS and notably uses it in "Sharif Returns" (S4E13).
Colt Government
In "Sandblast" (S4E07), Gibbs finds a Colt Government Model handgun in the store of the CIA informant Mamoun Sharif (Enzo Cilenti). Gibbs mentions that the handgun is ".38 Super, Colt", which means it's a Colt model chambered in .38 Super.
Colt M1911A1
In "Escaped" (S4E02), retired Navy sailor Mickey Stokes (Hal Holbrook) has his old M1911A1 stolen from him and then later pointed at him by Petty Officer Derrick Paulson (Brandon Barash).
In a continuity error, a suppressed CZ 83 pistol is briefly seen instead of Makarov when Namir Eschel (Eyall Podell) has a pillow put over his head in Season 4's premiere "Shalom" (S4E01).
Glock 17
The Glock 17 is another frequently-used handgun in the series. In Season 4's "Faking It", Glocks are carried by DC-Metro Police.
Glock 19
The Glock 19 is used by numerous characters in the series. NCIS Special Agent Michelle Lee (Liza Lapira) while undercover is seen holding a Glock in Season 4's "Once A Hero". Mike Franks uses one in the rescue of his daughter in law in Season 4's "Iceman".
Jericho 941 "Baby Eagle"
In Season 4's "Faking It", Russian arms dealer Arkady Kobach (V.J. Foster) lets his two tone Jericho 941 R fall when he sees that Mike Franks (Muse Watson) has the drop on him.
Makarov PM
A suppressed Makarov PM is used by Faatin Amal (Saba Homayoon) in Season 4's premiere "Shalom" (S4E01).
Walther PPK/S
A suspect holds the suppressed Walther PPK in "Singled Out".
FBI SWAT agents are armed with Heckler & Koch MP5A2's when raiding a suspected terrorist hideout in Season 4's premiere "Shalom" (S4E01).
IMI Micro Uzi
In a flashback, Ziva uses a Micro Uzi in a Mossad Kidon assassination in Paris in Season 4's premiere "Shalom" (S4E01).
Rifles
Colt M4A1 Carbine
The M4A1 carbine can be seen used by various US Military personnel and gunmen throughout the series.
Sniper Rifles
Remington 700PSS
Ziva uses a Remington 700PSS rifle while covering Ducky in "Blowback" (S4E14).
Shotguns
Remington 870 Police "Entry Gun"
In "Sandblast" (S4E07), Lt. Col. Hollis Mann is seen using a Remington 870 Police Entry Gun fitted with a saddle shell holder and forend weapon light when raiding a suspected terrorist hideout.