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 Colonel Sarah "Mac" Mackenzie (Catherine Bell) and Lieutenant Gregory Vukovic (Chris Beetem) as well as other military personnel.
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
The M4 Carbine is seen being used by Marines notably in "Death at the Mosque" (S10E18), with and without various attachments.
M16/AR-15 SP1 (with A2 Handguards)
In "This Just In from Baghdad" (S10E05), M16/AR-15 SP1 rifles with A2 handguards are seen in the hands of US Marines.
M16A1 (with A2 Handguards)
In "This Just In from Baghdad" (S10E05), some of the rifles carried by US Marines are M16A1's with A2 handguards.
Machine Guns
Browning M2
The Browning M2 is mounted on Marine humvees in Iraq, notably in "Death at the Mosque" (S10E18).
M249 SAW
The M249 SAW is used by Marines when advancing to their target in Season 10's "Death at the Mosque" (S10E18).
Other
M72A2 LAW
The M72A2 LAW is used by a Marine in "Death at the Mosque" (S10E18).
Mk 19 Grenade Launcher
The Mk 19 grenade launcher is briefly seen mounted on a Marine humvee in "Death at the Mosque" (S10E18).