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 Colonel Sarah "Mac" Mackenzie (Catherine Bell) and Rear Admiral A.J. Chegwidden (John M. Jackson) as well as other military personnel.
Browning Hi-Power
A Browning Hi-Power is used by British Forces in "Trinity" (S2E06). A Browning Hi-Power is pulled in "The Game of Go".
Former Navy SEAL Paul Bauwer (Bruce Weitz) holds a Ruger KP90 that he took off a robbery suspect in "The Guardian".
Shotguns
Remington 870 (USMC)
In "A Game of Go" (S2E10), Rabb takes a Remington 870 (which appears to be in the USMC configuration) from a cartel guard and holds it on the drug lord.
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 in the series. Rabb uses a SEAL's MP5-PDW to prove his point by shooting a courtroom ceiling in "Heroes" (S2E04). 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. In "Code Blue" (S2E13), HAMAS terrorists including Mustapha Ben Kessar (Francesco Quinn) are armed with MAC-11's as they take over a hospital. Harm is later seen with the weapon.
Sterling SMG
Sterling SMG's are used by British Forces in "Trinity". The footage seen is from the film In the Name of the Father.
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.
AKMS
In "Trinity" (S2E06), an IRA member is armed with an AKMS.
Colt AR-15A2 Government Carbine
In Season 2's premiere "We the People" (S2E01), Sergeant Riske (Sal Landi) a militia member, is seen armed with a Colt AR-15A2 Government Carbine fitted with a scope.
Marlin Model 336
In "Full Engagement" (S2E08), a poacher uses a Marlin Model 336 to open fire on Harm and Sarah. Harm also uses the rifle.