The Recon Marines carry Beretta 92FS (military designation, M9) pistols as their sidearms. Beretta M9s with early model Surefire 333R tactical flashlight are the standard sidearm for all the Navy SEALs. Stanley Goodspeed (Nicolas Cage) also uses a Beretta 92FS as his sidearm when infiltrating Alcatraz with Mason and the SEALs. Shortly after the ambush, 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 during the standoff with Capt. Darrow and the other Marines.
Beretta 92FS Centurion Inox
When FBI transport Mason to the hotel, Goodspeed is given a Beretta 92FS Centurion Inox by another FBI agent after he arrives in San Francisco and tells Womack (John Spencer) that he forgot his FBI-issue sidearm. Strangely, all of the other FBI agents in the movie also seem to be carrying 92 Centurions with Inox finishes, even though this pistol has never been issued to the FBI in real life (at the time the movie was made, the FBI would have been using SIG-Sauer and Smith & Wesson pistols).
Beretta 92SB
Captain Darrow (Tony Todd) 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.
Smith & Wesson 4506
While waiting for Hummel to fire one of his VX gas missiles, Capt. Frye (Gregory Sporleder) is seen with his Smith & Wesson 4506, spinning it on a steel stool.
Colt Government Model MK IV Series 80 Stainless
The main villain of the film, General Frank Hummel (Ed Harris) carries a stainless Colt MK IV Series 80 stainless as his sidearm of choice throughout the film. It is seen being pulled out by Hummel, who then shoots Sergeant Crisp during the confrontation. On this occasion, you can see written on the right side "Colt Government Model". This particular and rare version of MK IV has advanced vertical grooves from the beginning of the slide.
Submachine Guns
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.
Heckler & Koch MP5A3/A5
A Heckler & Koch MP5A3 with an SEF trigger group is held by SEAL Commander Anderson (Michael Biehn). A Heckler & Koch MP5A5 is also seen in the hands of one of the Navy SEALs. Mason commandeers one from a dead SEAL and uses it for about 1/3 of the film until he heads off to confront Hummel and stop him from killing the civilian.
(in an interesting note, the SEALs use Chalker Slings for their weapons, designed by Denny Chalker, plank-holder in SEAL Team SIX. Chalker also appears in the film as one of the SEALs (Boyer). Another of his teammates, Harry Humphries, is the Navy Admiral who asks to bring in the SEAL leader after the initial ransom call)
Heckler & Koch HK94 (converted to resemble the MP5)
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 receiver and a right handed only selector switch with the old 0-1-2 switch.
A Heckler & Koch SP89 by the SEAL Boyer during the failed attempt to save the hostages. It seems to be fitted with the folding stock of MP5K-PDW, and was evidently converted to full-auto.
Rifles
LAR Grizzly Big-Boar
When Private McCoy's M60E3 is empty, he picks up a .50 BMG LAR Grizzly Big-Boar bolt-action rifle to shoot Goodspeed. He is knocked off the roof by Mason before he can use it, though.
M14 Rifle
A Marine honor guard during the opening credits can be seen briefly holding the M14 rifle.
M16A2
Marines at the funeral use real M16A2 rifles for the 3 volley 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.
(Fake) Colt XM177
Colt XM177 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 XM177s in the film all have 10" barrels and bulky 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. What this means is that none of them are factory XM177 variants. Like most of the "XM177s" seen in Hollywood, the upper receivers of the guns in this movie are most likely taken from civilian AR-15 carbine variants that have had their barrels chopped and fake XM177-style flash hiders welded on. The lower receivers (all of which seem to lack "fencing" of more modern M16 variants) may either be from genuine XM177s, or they may again be civilian AR15 Sporter-1 lowers converted to auto. Yet another example of movie "Franken-guns" built from the parts of many weapons.
A notable goof is that the receivers of the guns held by individual characters change throughout the film. For instance, the XM177 handed to Goodspeed by Mason clearly has an A2 receiver when he first gets it, but later, it has an A1 receiver. Captain Frye's (Gregory Sporleder's) XM177 also undergoes various receiver changes - in the shower room scene, it has an A2-style receiver, while in later scenes it has a forward assist and brass deflector but no A2-style rear sight, and still later it has just the forward assist (A1-style receiver).
Shotguns
Mossberg 590 Combat Shotgun
Hummel's men uses a Mossberg 590 to fire a zip line during the opening assault on the Marine base.
Remington 870
A SEAL can be seen using a shortened tactical Remington 870 shotgun.
Machine Guns
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.
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.
M203 Grenade Launcher (Standalone)
During the opening assault on the Marine base, one of Hummel's men disables a Marine in the guard tower with a beanbag round fired from a standalone M203 grenade launcher.
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 SEALs. They could also be Hornet's nest rounds, which is a grenade round with 8 .22 long rifle bullets inside.
Crossman CO2 Air Gun
Hummel's marines including Private Scarpetti (Jim Maniaci) use Crossman CO2 Air Guns loaded with tranquilizer rounds when infiltrating the base containing the VX gas.
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.
"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.