While in reality the Beretta M9 is the standard issue sidearm for US military, the Beretta 92FS is the weapon seen used in the series by the US military personnel. The handgun is used by Commander Harmon "Harm" Rabb, Jr. (David James Elliott), Lieutenant (junior grade) Meg Austin (Tracey Needham) and CDR Alison Krennick (Andrea Thompson).
Browning Hi-Power
A Browning Hi-Power is pulled by an Iraqi officer in "Scimitar" (S1E09).
Grendel P-10
A Grendel P-10 fitted with a suppressor is used by the assassin codenamed "Hemlock" (Jack Conley) in "Hemlock"(S1E15).
Makarov PM
The Makarov PM is used by several characters in the series. Colonel Yang Chee (Aki Aleong) holds a Makarov in "The Prisoner" (S1E20).
Smith & Wesson 5906
A Smith & Wesson 5906 was the sidearm used by the local sheriff's deputies in "Survivors".
Ruger KP90
An assassin opens fire on Rabb's apartment with a stainless and suppressed Ruger KP90 in "Deja Vu".
In "Sightings" (S1E11), a Remington 870 Field shotgun with a sawed-off barrel and pistol grip is seen in the hands of J.D. Gold (Wings Hauser) and later is used by Rabb.
Remington 870 Police
Sheriff's Deputy Terence Hodge (Steven Barr) is seen taking out a Remington 870 Police shotgun in "Survivors" (S1E18).
Submachine Guns
Heckler & Koch MP5N
The Heckler & Koch MP5N (with the Navy trigger group) is used by SEALs, Marines, and other various tactical units in various episodes in the series, often fitted a Surefire tactical weaponlight.
Heckler & Koch MP5K-PDW
The Heckler & Koch MP5K-PDW is seen used frequently over the series, most notably by Rabb to rescue Lieutenant Painter in the Season 1's "Defensive Action" (S1E13). These are MP5K-PDWs due to the 3 lug barrels and folded stock.
MAC-11
The MAC-11 is a frequent submachine gun seen in the series. Rabb and several bodyguards were armed with MAC-11s in "War Cries" (S1E07).
SA Vz.61 Skorpion
The SA Vz.61 Skorpion is seen being used by Russian Secret Service in "Hemlock", and by members of The Shining Path in "War Cries".
Rifles
AK Variants
Kalashnikov and Norinco Rifles have been seen during the show's ten seasons. In the episodes set in Russia, Chechnya, Cuba, Iraq, China, etc, as well as flashbacks to the Korean War, Vietnam, and the Cold War, many varieties of Kalashnikov rifles have been seen, as well as the Chinese manufactured Norinco rifles. Unlike most movies and television shows JAG was usually pretty accurate about having the right rifle type for the locations.
XM177E2 'Colt Commando'
A militia leader is seen carrying a XM177E2-style carbine when engaging Marines in "Brig Break". Another XM177 with a M203 grenade launcher is seen carried by SEAL Chief Petty Officer Shipp (Bobby Hosea) in "Black Ops".
MGC Replica M16 rifle
A number of characters were seen carrying MGC M16 Replica rifles for scenes where they didn't carry the blank-firing M16 rifles.
M16A1
M16A1's are frequently seen in the flashbacks to Vietnam, such as in the episode "Survivors".
M16A1 (with A2 handguards)
Various styles of the M16 rifle series appeared in JAG during the show's long run. M16A1s with A2 hand guards were frequently used to simulate M16A2s. These guns make sense in JAG, because the military does use a lot of "Frankenstein" M16s. The Air Force being the worst offender, but they can be found in service with all branches.
Can also be seen in several episodes of Season 7 including "Code of Conduct" (being used by Navy SEALs), "Tribunal" (incorrectly shown being used by US Army Special Forces), and "In Country" (seen being carried by Harm, Mac, and Gunnery Sergeant Galindez (Randy Vasquez).
M1903 Springfield
In "Deja Vu" (S1E05), a Marine Silent Drill Platoon seen in Washington, D.C. perform their drills with M1903 Springfield rifles with bayonets. Some of this footage is from the 1992 film A Few Good Men.
Sniper Rifles
Remington 700PSS
Gunnery Sergeant Crockett (Stephen McHattie) takes aim with an Remington 700PSS (used as a substitute for the M40) in "High Ground". Several SWAT snipers are seen armed with the rifle throughout the series.
Remington 700
A militia member is seen using a Remington 700 rifle when engaging Marines in "Brig Break".
In Season 1's "War Cries", a Humvee-mounted Browning M2 50 cal is fired by Gunnery Sergeant Granger (John Wesley Shipp). The M2HB is seen mounted on Marine M1A1 Abrams tanks in Season 3's "Father's Day" (S3E14). The M2 is also mounted on Marine humvees in Iraq, notably in Season 10's "Death at the Mosque".
DShK (Mocked up Browning M2)
A Browning M2 mocked up to resemble the DShK heavy machine gun is used by a Serb soldier to shoot at the CAG's F-14 in the pilot episode.
M230 Chain Gun
In "Scimitar", an AH-64 Apache is seen using its M230 Chain Gun to engage a Hind helicopter. The footage seen in the episode was taken from the film Fire Birds.
Other
SA-7 Grail
A Serb soldier uses a SA-7 Grail to shoot down a C-130 in the pilot episode.
FIM-92A Stinger
A FIM-92A Stinger was stolen and used in Season 1's "Brig Break".
Type 69 RPG
The Type 69 RPG fitted with a PGO-7 scope was used by Shining Path terrorists in "War Cries".