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), Lt. Colonel Sarah "Mac" Mackenzie (Catherine Bell) and Rear Admiral A.J. Chegwidden (John M. Jackson).
Walther PPK/S
A Walther PPK/S is pulled in "Rogue" and "The Colonel's Wife".
Shotguns
Mossberg 500
A Mossberg 500 shotgun is held by an ERT officer in "The Colonel's Wife" (S5E08).
Rifles
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.