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, at least one of which is 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. 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 92SB
One of the Marines, Captain Darrow (Tony Todd) is seen using an older 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 92 Centurion Inox
During the hotel scene Goodspeed is given a Beretta 92 Centurion with an Inox finish by another FBI field agent after he arrives in San Francisco and tells Womack that he forgot his FBI-issue sidearm.
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)
Many of the Marines under General Hummel (Ed Harris) are armed with M16A1 assault rifles fitted with M16A2 handguards. They are easily noticed as A1 models by the lack of a shell deflector, older forward assists, and fully-automatic firing modes. Some 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).
M203 Grenade Launcher
Some of the Marines have M203 grenade launchers mounted on their M16s and CAR15s. Captain Darrow (Tony Todd), for instance, has an M203 on his M16A1 which is seen prominently during the scene where he confronts Goodspeed in the lighthouse.
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.
Springfield Armory 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.
Heckler & Koch MP5A3/A5
Heckler & Koch MP5A3 submachine guns are used by the Navy SEALs during the failed rescue mission of the prison. They have Surefire dedicated forend weaponlights. Mason wields an MP5A3 he commandeers from a dead SEAL, and uses it in the first half of the movie.
A handful of the MP5s used by the SEALs also appear to have the 4-position trigger group (for safe, semi, 3-round burst, and full-auto) and smooth lower reciever, which makes them MP5A5s rather than A3s.
A SEAL can be seen using a shortened tactical Remington 870 shotgun.
H&K 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 Defense Technologies (DefTech) 37mm launcher is used by one of the Marines in the shower room, apparently as an HE grenade launcher. It would be useless to use as the rounds would not detonate in such close proximity and if they did, it would be dangerous to him and his fellow men.
M26 Handgrenade
Cpt. Frye can be seen with two M26 hand grenades which he throws at Mason in an attempt to kill him. Mason jumps into a bathtub to avoid the blasts.
M60E3
A Marine 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.
HOHOHOHO
LAR Grizzly Big-Bore
When the Marine'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 officer, 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.