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" and "Legend, Part II".
In Season 6's "Legend, Part I" and "Legend, Part II", NCIS Special Agent Kensi Blye (Daniela Ruah) uses a SIG-Sauer P239 to threaten a group of bangers.
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.
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".
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."
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.
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.
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.
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".
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.
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".
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).
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".
A terrorist in "Dead Reckoning" (S6E15) uses a Skorpion SA Vz 61 to shoot at Trent Kort before being killed by him. 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.
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).
The SIG SG 552 is used by Sam, Kensi and other NCIS agents in Season 6's "Legend Pt. 2" (6x23) when they raid a garage that is the headquarters of a suspected terrorist cell.
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 Season 6's "South by Southwest".