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 Lt. Commander Harmon "Harm" Rabb, Jr. (David James Elliott), Major Sarah "Mac" Mackenzie (Catherine Bell) and Rear Admiral A.J. Chegwidden (John M. Jackson).
An engraved nickel Beretta 950 Jetfire is seen given to RADM Chegwidden by his ex-wife Marcella (Barbara Carrera) in "Going After Francesca" (S4E04). It is later used by the admiral's daughter Francesca (Guiliana Santini) in the same episode.
Chegwidden and Harm are seen using Mossberg 590 shotguns in "Going After Francesca" (S4E04). While it's mentioned that the shotguns have speedfeed stocks, these shotguns appear to not have them.
Machine Guns
RPD
An RPD machine gun is seen mounted in a Soviet helicopter that searches for the downed aircraft flown by Rabb in "Gypsy Eyes" (S4E01).
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.
M4A1 Carbine
Lt. Curtis Rivers (Montel Williams) is seen using an M4A1 carbine in "Rivers' Run" (S4E15). The M4A1 seen in the episode is fitted with a C-More sight and an early Surefire RIS forearm; this is most likely one of the same rifles seen in Soldier (which had the same armorers as this show).
Sniper Rifles
Remington 700 (Choate Ultimate Sniper Stock)
A suppressed Remington 700 bolt action sniper rifle fitted in the Choate Ultimate Sniper Stock is used by RADM Chegwidden in "Soul Searching" (S4E22).
Remington 700SPS
A Remington 700SPS is held by an FBI sniper in "Rivers' Run" (S4E15).