The SIG-Sauer P228 is the main sidearm of nearly all the NCIS agents in the series including Special Agents Leroy Jethro Gibbs (Mark Harmon), Anthony DiNozzo (Michael Weatherly), Timothy McGee (Sean Murray), and Ziva David (Cote de Pablo). The NCIS agents who are assigned to the Office of Special Projects in Los Angeles also carry P228's in "Legend, Part I" (S6E22) and "Legend, Part II" (S6E23).
SIG-Sauer P239
In "Legend, Part I" (S6E22), NCIS Special Agent Kensi Blye (Daniela Ruah) uses a SIG-Sauer P239 to threaten a group of bangers.
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. In "Deliverance" (S6E15), Ziva fires one on a Marine weapons range and claims to prefer the SIG. She also upsets the misogynistic range sergeant on duty, who doesn't expect women to know anything about handguns, by showing him his sight is off by a few millimeters.
Beretta 92FS Inox
In Season 6's "Deliverance", a gun dealer is seen showing a Beretta 92FS Inox to a customer, stating it's "Homie's best friend 9mm, it's Italian, 15 plus 1 in da tube".
Glock 17
The Glock 17 is another frequently-used handgun in the series. Mossad Officer Michael Rivikin (Merik Tadros) pulls a Glock 17 on Callen during the the Season 6's "Legend, Part 2."
Glock 17 (Full Auto Conversion)
In Season 6's "Legend, Part 2", a two-toned Glock 17 converted to full auto with a 33 round magazine is used by the lead terrorist Haziq Khaleel (Nick Tarabay) in an attempt at repelling the OSP raid team.
Glock 19
The Glock 19 is used by numerous characters in the series. In "Dead Reckoning" (S6E20), Deputy US Marshals draw their Glocks on Trent Kort. Perry Sterling (Christian Clemenson) also holds the Glock.
Glock 21
In "Dead Reckoning" (S6E20), CIA Agent Trent Kort (David Dayan Fisher) uses a Glock 21 during a shootout at the beginning of the episode. After they are dead he picks up the dead guy's Smith and Wesson Tactical 9x19mm and wipes his Glock 21 for prints and puts it the hands of the dead terrorist.
Ruger Mk I
In Season 6's "South by Southwest", a Ruger Mk I is used to assassinate an NCIS agent.
Smith & Wesson SW1911PD
Mike Franks (Muse Watson) carries a Smith & Wesson SW1911PD with the full 5" barrel as his sidearm. What differentiates the PD model are the front serrations on the slide that's similar to those in such handguns as the Kimber. The pistol also has a desert tan Crimson Trace grip-mounted laser sight. The SW1911PD is also used in the Season 6 episode "Deliverance".
Smith & Wesson 5906
In Season 6's "Dead Reckoning" (S6E20), CIA Agent Trent Kort (David Dayan Fisher) takes a Smith & Wesson 5906 from a terrorist that he shot after planting his Glock on the dead guy.
Revolvers
Colt Python
In "Deliverance" (S6E15), a gun dealer shows a Colt Python to a customer.
Smith & Wesson Model 10
In "Capitol Offense" (S6E03), McGee falls into a small pond where he finds a Smith & Wesson Model 10 that may have been used in a Navy lieutenant's murder. DiNozzo calls it a "Smith & Wesson. 38 Kit".
Smith & Wesson Model 37
A nickel Smith & Wesson Model 37 Airweight revolver is used to kill a bully on a Navy base in "Hide & Seek" (S6E19). Checking out its violent history causes Abby Sciuto (Pauley Perrette) to label it an "evil gun" and describe it as possessed (as it was used in convenience store hold-ups and other crimes each time it changed hands).
Smith & Wesson Model 340PD
Ziva carries a Smith & Wesson Model 340PD as her backup gun, which she carries in an ankle holster. She dual wields the revolver along with her SIG in "Dead Reckoning" (S6E20).
In "Deliverance" (S6E15), a gun dealer shows an Intratec TEC-9 to a potential client, saying "TEC-9, full auto, empty a clip in 4 seconds" and encourages him to fire it, the burst hitting the roof of the abandoned warehouse and causing the body of an already-slain Marine to fall through the skylight. It was also seen in Season 3's "Iced".
Skorpion SA Vz.61
In "Dead Reckoning" (S6E15), a terrorist opens fire on Trent Kort with a Skorpion SA Vz 61. Kort then uses the Skorpion to shoot another terrorist. While usually chambered in .32 ACP, there is evidence that Vz61 clone pistols were chambered in .380 in the 1980's.
Rifles
AKM
The AKM is a frequent weapon used by terrorists and suspects in the series.
Colt M4A1 Carbine
The M4A1 carbine can be seen used by various US Military personnel and gunmen throughout the series.
Colt Model 933
In "Cloak" (S6E08), US Navy security guards are seen armed with the Colt Model 933 rifle fitted with a weaponlight.
Henry Rifle
What appears to be a Winchester rifle converted to resemble a Henry 1860 rifle is carried by Sheriff Boyd (Lance Henriksen) and then used by Gibbs to shoot down a helicopter in "South by Southwest" (S6E17). The rifle, which is referred to as a "Henry" by Boyd, is seen fitted with a Vernier sight and has a longer octagonal barrel of a Henry, but is side loading like a Winchester.
M16A2 Rifle
The M16A2 rifle is notably carried by US Marines in several episodes as well as other characters throughout the series. Bart Lemming (Tim Guinee) takes aim with a scoped M16A2 from a helicopter in "South by Southwest" (S06E17).
SIG SG 552
The SIG SG 552 is used by Sam, Kensi and other NCIS agents in "Legend, Part II" (S6E23) when they raid a garage that is the headquarters of a suspected terrorist cell.
Winchester 1873
In "Heartland" (S6E04), a Winchester Model 1873 rifle is owned by Jackson Gibbs (Ralph Waite), who keeps it loaded on the wall in his store. Agent Gibbs mentions that his father never allowed him to touch the rifle.
Winchester Model 1892
Artist Dina Risi (Mira Furlan) aims what appears to be a Winchester Model 1892 rifle at Gibbs and DiNozzo when they come looking for her in "South by Southwest" (S6E17).
Sniper Rifles
M40A1 Sniper Rifle
An M40A1 sniper rifle was the rifle used by Gibbs in his Marine days and he now keeps it in a case in his basement. In "Deliverance" (S6E15), Gibbs experiences a flashback where he is seen with the rifle.
Shotguns
12 Gauge Double Barreled Shotgun
The team enters a garage where the "CyberVid Killer" is forced to hold a 12 Gauge Double Barreled Shotgun in "Murder 2.0" (S6E06).
Other
Advanced Taser X26
What appears to be an Advanced Taser X26 is used by a security guard on McGee in "Silent Night" (S6E11).