A marine at the funeral during the opening credits can be seen briefly holding an M14 rifle.
Beretta 92FS
The Recon Marines carry Beretta M9FS Pistols as their sidearms, all custom fitted with wooden grips. Beretta M9s are the standard side arm for all the Navy SEALs including Stanley Goodspeed (Nicolas Cage), all with tactical flashlight attachments.
Beretta 92FS Inox
During the hotel scene Goodspeed is given a Beretta 92FS Inox from another FBI field agent.
M16A2
Marines at the funeral use real M16A2 rifles for the 21 gun salute.
It is a goof that they rack the bolts to fire them as funeral guns are usually real guns fitted with a blank firing adapter on the muzzle to allow enough gas pressure to cycle the bolt(as real guns have heavier bolt springs than blank guns. Blank guns need lighter springs to allow the gas pressure to cycle low pressure blank rounds.)
M16A1 w/ M16A2 handguards.
The Marines can be seen armed with M16A1 rifles fitted with M16A2 forend handguards. They are easily noticed as A1 models by the lack of a shell deflector, older foward assists, and fully-automatic firing modes.
M16A1 with M203 Grenade Launcher
Captain Darrow's weapon of choice is an M16A1 fitted with a 40mm M203 launcher.
Colt Commando
Is seen being used by multiple Marines in multiple scenes. Mason and Goodspeed take two for themselves later in the film.
Colt M1911A1
The main villain of the film, General Frank Hummel (Ed Harris) carries a stainless Springfield Armory M1911A1 as his sidearm of choice throughout the film. It is seen being pulled out by Hummel, who then shoots Sergeant Crisp during the confrontation.
H&K MP5A3
Used by the Navy SEALs during the failed rescue mission of the prison. They have tactical flashlights mounted in the foregrips. John Mason (Sean Connery) uses an MP5A3 he commandeers from a dead SEAL, and uses it in the first half of the movie.
MP5K
Seen used by one of the SEALs in the shower room, briefly.
Remington 870
A SEAL can be seen using a shortened tactical Remington 870 shotgun.
H&K SP89
Used by one of the SEALs during the failed attempt to save the hostages.