In "Forced Entry" (S2E09), Laura Rowens (Megan Ward) uses a Beretta 85F to shoot a man she thought was going to attack her. In "Conspiracy Theory" (S2E19), Catherine Reynolds (Brigid Brannagh) is seen holding the Beretta on her partner in crime.
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 the Season 2 premiere "See No Evil" (S2E01), kidnapper Kyle Grayson (William Mapother) holds one on his hostage while in a standoff with NCIS agents.
Colt M1911A1
In "Vanished" (S02E03) Marine helicopter pilot Captain Todd Newell (Rob Boltin) carries a M1911A1 while hiding out in the Virginia forest and stalking his brother's murderer. In "Call of Silence" (S2E07), Iwo Jima veteran Ernie Yost (Charles Durning) brings his M1911A1 to NCIS headquarters to turn himself in for possibly murdering a fellow Marine during the war. In Season 2's "Dark Water", private investigator Monroe Cooper (Mike Starr) is caught faking the murder of an accident victim, using a M1911A1 from the home of the primary "suspect."
Glock 17
The Glock 17 is another frequently-used handgun in the series. In Season 1's "Enigma", FBI Special Agent Tobias Fornell (Joe Spano) is seen drawing a Glock. In Season 2's "Terminal Leave," Navy Lt. Commander Michaela "Micki" Shields (Mary Page Keller) keeps a Glock in her home.
Glock 17L
In "Witness" (S2E14), a Glock 17L was found in the convertible sofa bed used by Petty officer Keith Dylan/Robert J. Thorn. It was misidentified as a SIG-Sauer and can be clearly seen in multiple other scenes as a Glock, most clearly when being test-fired into a bullet capture chamber by Abby Sciuto (Pauley Perrette).
Glock 19
The Glock 19 is used by numerous characters in the series.
Para Ordnance Companion C7.45
In Season 2's "Chained", Tony uses a Para Ordnance C7.45 (as evidenced by the factory Para grips and the LDA hammer and trigger).
Smith & Wesson 5906
A terrorist, disguised as a trooper, uses a S&W 5906 to gun down the naval officers in Season 2's "Twilight".
Revolvers
Ruger GP100
In "Pop Life" (S2E16), club owner Ian Alfred "Bulldog" Hitch (Steven Brand) is seen using a Ruger GP100 to threaten one of his dancers, Samantha "Jade" King (Mya Harrison).
Smith & Wesson Model 60
In Season 2's "Terminal Leave", DiNozzo is seen carrying a Smith & Wesson Model 60 as his backup weapon when jogging with a Navy commander.
Smith & Wesson Model 66
A Smith & Wesson Model 66 is pulled by distraught housewife Greta Boyen (Rebecca Staab) in Season 2's "Terminal Leave".
Rifles
AKM
The AKM is a frequent weapon used by terrorists and suspects in the series.
AKMS
In the Season 2 finale "Twilight", several terrorists can be seen firing AKMS rifles at Gibbs and the team to no avail. The weapon is also used by various other characters in the series.
Arisaka Type 99 Rifle
Imperial Japanese soldiers are seen with the Type 99 Arisaka Rifle as Ernie Yost (Charles Durning) remembers his time on Iwo Jima in Season 2's "Call of Silence" (S2E07).
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
Bravo 51
The Bravo 51 is used by Ari Haswari (Rudolf Martin) in the Season 2 finale "Twilight".
In Season 2's finale "Twilight" (S2E26), Gibbs (Mark Harmon) uses a police Remington 870 to flush out the terrorists in the warehouse. Kate (Sasha Alexander) uses it during the shootout before running out of ammo and tossing it to take a bullet for Gibbs.