A Marine at the funeral during the opening credits can be seen briefly holding an M14 rifle.
Beretta 92FS
The Recon Marines carry Beretta 92FS (military designation, M9) pistols as their sidearms. Beretta M9s are the standard side arm for all the Navy SEALs including Stanley Goodspeed (Nicolas Cage), all with tactical flashlight attachments. Goodspeed points his at John Mason (Sean Connery), who swipes it out of his hand, but later gives it back to Goodspeed to defend himself with, and he uses it notably in the underground tunnels to kill one Marine, with little hesitation, as Mason notes.
Beretta 92FS Inox
Major Baxter (David Morse) uses a Beretta 92FS Inox as his sidearm. He draws it on Hummel before turning the gun on Darrow and firing at him before being gunned down by the other Marines.
Beretta 92SB
One of the Marines is seen using an older Beretta 92SB (which has a rounded trigger guard, rather than squared, like on the 92FS/M9) with wood grips during the scene in which Hummel and his men use a hostage to draw Goodspeed and Mason out of hiding.
Beretta 92FS Centurion Inox
During the hotel scene Goodspeed is given a Beretta 92FS Centurion Inox by another FBI field agent after he arrives in San Francisco and tells Womack (John Spencer) that he forgot his FBI-issue sidearm.
Smith & Wesson 4506
While waiting for Hummel to fire one of his VX gas missiles, a Marine is seen with his Smith & Wesson 4506, spinning it on a rotating table.
M16A2
Marines at the funeral use real M16A2 rifles for the 21 gun salute.
M16A1 (w/ M16A2 handguards)
Many of the Marines under General Hummel's (Ed Harris) command are armed with M16A1 assault rifles fitted with M16A2 handguards. They are easily noticed as A1 models by the lack of a brass deflector and elevation-adjustable rear sight, older forward assists, and fully-automatic firing modes. Most of them have tactical flashlights installed on the barrels.
Colt Commando variants
Colt CAR-15 Commando look-a-like rifles seen being used by many of the Marines. Mason and Goodspeed take two for themselves later in the film. The Commandos in the film all have 10" barrels and older-style flash suppressors, but also have various receiver styles. Some have A1 receivers, others have A2 receivers, and others have the forward assist and brass deflector but not the A2-style rear sight. Some have tactical flashlights on the barrels.
A notable goof is that the receivers of the guns held by individual characters change throughout the film (for instance, the Commando handed to Goodspeed by Mason clearly has an A2 receiver when he first gets it, but later, it has an A1 receiver).
While CM203 flare launchers dominate the film, Cpt. Darrow's rifle is fitted with a real M203 grenade launcher, likely because he is a main character. Throughout the film, the rifle this launcher is fitted to changes from a slab-side M16 (SP1), to an M16A1, and at one point, even a Colt CAR-15 Commando, although it is fitted with a CM203 launcher instead.
MAC-10
Hummel can be seen holding a MAC-10 in a Vietnam service picture. This image is actually taken from one of Ed Harris' earlier film roles, the Charles Bronson vehicle Borderline.
Colt M1911A1
The main villain of the film, General Frank Hummel (Ed Harris) carries a stainless Colt 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.
A handful of the MP5s used by the SEALs also appear to be chopped and converted 16" barrel civilian semi-auto Heckler & Koch HK94s with the barrels chopped down and converted to full auto. These lack barrel lugs and paddle magazine releases, as well as no push pin lower reciever and a right handed only selector switch with the old 0-1-2 switch.
A SEAL can be seen using a shortened tactical Remington 870 shotgun.
Heckler & Koch SP89
A Heckler & Koch SP89 by one of the SEALs during the failed attempt to save the hostages. It seems to be fitted with the collapsible stock of an MP5A3, and was evidently converted to full-auto.
DefTech Launcher
What appears to be a DefTech 37mm launcher is used by Private McCoy (Steve Harris) in the shower room, firing shotgun like rounds at the Marines. They could also be Hornet's nest rounds, which is a grenade round with 8 .22 long rifle bullets inside.
A Marine in the morgue tries to pull the pin on an M18 Smoke Grenade to throw at Mason as a last ditch effort in killing him before Mason shoots out an air vent above him which crushes his head. In reality, a smoke grenade doesn't pose a threat for obvious reasons.
M60E3
Private McCoy (Steve Harris) can be seen firing an M60E3 machine gun at Goodspeed when he disables the last rocket. Mason picks it up and knocks the shooter off the roof with it.
LAR Grizzly Big-Bore
When Private McCoy's M60E3 is empty, he picks up a .50 BMG LAR Grizzly Big-Bore bolt-action rifle to shoot Goodspeed. He is knocked off the roof by Mason before he can use it, though.
"The Protector"
When Goodspeed is messing around in his office, he shoots a flip down target with a suction dart spring gun labeled "The Protector". It appears to be based off a Mossberg 500 "Cruiser" with barrel ribbing.