A SIG-Sauer P229 is carried by a US Coast Guard officer in "Safe Harbor" (S9E05).
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.
"Blackhand"
A prototype special operations pistol called the "Black Hand" was used in several murders by an ex-military analyst turned assassin in "The Penelope Papers" (S9E03). It's a prop pistol that is based on the SP-21 Barak.
Desert Eagle Mark XIX
In "Housekeeping" (S9E12), ex-Watcher agent Casey Stratton (Scott Wolf) fires a Desert Eagle. Ziva says that it has .50 caliber bullets, which indicates that its caliber is the .50 Action Express.
Glock 17
The Glock 17 is another frequently-used handgun in the series.
Jericho 941
What appears to be a Jericho 941 pistol is used by a FBI agent in "Housekeeping" (S9E12).
Smith & Wesson 3913
A suppressed Smith & Wesson 3913 is seen used at the beginning of "Newborn King" (S9E11).
Revolvers
Smith & Wesson Model 37
In "Restless", Smith & Wesson Model 37 Airweight was seen beside ex-con Curtis when Gibbs and the NCIS team (except Ziva) were approaching him on the roof of a taco restaurant.
Smith & Wesson Model 340PD
Ziva continues to carry a Smith & Wesson Model 340PD as her backup gun, which she carries in an ankle holster. She often is seen dual-wielding the revolver along with her SIG, this time in "Newborn King" (S9E11).
Submachine Guns
Heckler & Koch MP5A3
In "Housekeeping" (S9E12), an FBI SWAT agent is armed with the Heckler & Koch MP5A2 fitted with an ACOG scope,weaponlight and laser sight (it's possible that this weapon is an airsoft replica).
Heckler & Koch MP5SD2
A Heckler & Koch MP5SD2 is seen in Season 9's "Desperate Man" when Abby shows Gibbs a photo of the SD2.
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. In "Engaged, Part II" (S9E09), US Marines as well as Gibbs and Ziva are armed with M4A1's during a raid in Afghanistan.
Colt Model 933
US Coast Guard officers carry Colt Model 933 rifles while checking out a deserted ship in "Safe Harbor" (S9E05).
Heckler & Koch G36C
A Heckler & Koch G36C with a mounted suppressor on the barrel is seen in Season 9's "Enemy on the Hill" (S9E04) when Gibbs and Tony uncover the assassin's hidden arms stash in his garage.
M14
The ceremonial soldiers who guard the Tomb of the Unknown Soldier are seen holding M14 rifles in "Engaged, Part I" (S9E08).
Sniper Rifles
Accuracy International L96A1
The Accuracy International L96A1 is one of the sniper rifles found in an assassin's hidden arms stash in "Enemy on the Hill" (S9E04).
Ruger M77
A Ruger M77 is one of the sniper rifles found in an assassin's hidden arms stash in "Enemy on the Hill" (S9E04).
A Marine is briefly seen using an M249 SAW in "Engaged Part II" (S9E09).
Browning M2
A remote-operated Browning is seen mounted atop a Marine Cheetah in "Engaged, Part II" (S9E09).
Heavy Weapons
Airtronic RPG-7
In "Housekeeping" (S9E12), ex-Watcher operator Casey Stratton (Scott Wolf) can be seen firing an Airtronic RPG-7, a modernised US manufactured version of the RPG-7.