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.
Glock 17
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.
Glock 19
The Glock 19 is used by numerous characters in the series.
Col. Will Ryan (Terry O'Quinn), Gibbs former CO, owns and uses an Interarms imported Walther PPK/S in "Enigma" (S01E15).
Revolvers
Smith & Wesson Model 66
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.
Submachine Guns
Heckler & Koch MP5K-PDW
In the series premiere "Yankee White" (S1E01), an Al Qaeda sleeper takes a Heckler & Koch MP5K-PDW from the armory of Air Force One.
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.
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.
M16A2 Rifle
The M16A2 rifle is notably carried by US Marines in several episodes as well as other characters throughout the series.
Sniper Rifles
Blaser 93 Sniper Rifle
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".
Shotguns
Remington 870 (Police)
Kate is seen using a Remington 870 Police version with a dedicated forend weapon light to wound a suspect that took her SIG in Season 1's "UnSEALed".
Savage 512 O/U Gold Wing shotgun
A Savage 512 O/U Gold Wing shotgun is seen used by former Ensign Randy Wiles in Season 1's "The Curse".
Machine Guns
M60E3 Machine Gun
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.
Heavy Weapons
FIM-92A Stinger
An FIM-92A Stinger is seen in the weapons cache Col. Will Ryan (Terry O'Quinn) takes Gibbs to see in Season 1's "Enigma".
M72A2 LAW
A crate of M72A2 LAW's in seen in Season 1's "Split Decision".
M136 AT4
In Season 1's "Split Decision", an M136 AT4 is seen being put up for purchase on the internet.
M141 SMAW-D
In Season 1's "Split Decision", an M141 SMAW-D is seen being put up for purchase on the internet.
Norinco Type 69 RPG
In "Enigma" (S1E15), a Type 69 RPG is also seen in Col. Ryan's cache.