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 Season 1's "Missing" (S1E20), Major Joe Sacco (Derek Webster) holds a Beretta as he looks for Dinozzo in the sewer.
The Glock 17 is another frequently-used handgun in the series. In "Enigma" (S1E15), FBI Special Agent Tobias Fornell (Joe Spano) is seen drawing a Glock.
A Smith & Wesson Model 66 is said to have been used by Amanda Reed (Jamie Luner) in "Dead Man Talking" (S1E19). Gibbs referred to it as being "small, and easy to conceal." However, this is an error since the image of the gun that flashes on the lab screen (a stock product photo from the S&W catalog) is a Smith & Wesson Model 60, not the Model 66. The Model 60 is much more concealable than the larger framed Model 66.
In the series premiere "Yankee White" (S1E01), an Al Qaeda sleeper takes a Heckler & Koch MP5K-PDW from the armory of Air Force One.
Error creating thumbnail: File missingMP5K 9x19mm with the PDW-style folding stock attached, commonly used in films to emulate the PDW. The real MP5K-PDW, illustrated below, is distinctive in having the longer barrel and the newer trigger group.Error creating thumbnail: File missingIn the series premiere "Yankee White" (S1E01), Gibbs finds MP5K-PDW's in the Air Force One armory. This episode was filmed on the same set used for Air Force One, a film which Gibbs even mentions in the episode.Error creating thumbnail: File missingThe sleeper is taken down while holding the MP5K-PDW.
Heckler & Koch MP5A3
In "Enigma" (S1E15), Col. Will Ryan (Terry O'Quinn) takes an Heckler & Koch MP5A3 from one of his captors. In Season 1's "Split Decision", Gibbs goes undercover as an arms dealer, and uses a Heckler & Koch MP5A3.
In Season 1's "One Shot, One Kill", wannabe sniper Kyle Hendricks (Noah Segan) can be seen armed with a Blaser 93 sniper rifle, equipped with a bipod and custom muzzle brake. It is also one of the sniper rifles seen in Abby's lab in "Kill Ari, Part I".
In Season 1's "Split Decision", here Gibbs is undercover as an arms dealer, several short-barreled M60E3 machine guns can be seen; Gibbs bringing them to make a sale, however the ones he brought to 'sell' didn't have firing pins.