The fictional EM-1 rifle (EM standing for "Electro Magnetic") is used several times throughout the film. It is said to fire aluminium rounds at close to the speed of light, which is dubious for all manner of reasons; power consumption and heating would both be impossible to deal with in an infantry weapon, but the main issue would be how a C-fractional bullet would interact with the air around it. The projectile would be superheated almost instantly and burn up before it left the barrel, with the gun effectively firing a stream of plasma that would rise and dissipate; the result would be more like a hot steam gun than a projectile weapon. If it didn't, the projectile would interact with the atmosphere like a large meteor, creating a massive superheated trail that behaved like a directional nuclear explosion, including wake radiation in the area behind it. Far from throwing victims into the air, it would drill a hole through them so cleanly and quickly they'd barely notice in the instant before they and the entire surrounding area were obliterated by the wake. The shooter would likely end up with an EM-1 shaped hole in them and an equally large trail of destruction going in the opposite direction from the gun shooting itself backwards with similar velocity to the projectile.
The weapon is fitted with a variable magnification "X-Ray" scope, allowing the user to see through solid walls and showing human targets as skeletons, with the user able to mark his shot to their visible beating heart. The scope is a Hollywood invention; any X-Ray that could pass through steel, brick or concrete would not reflect off soft tissue or bone and pass through denser material again to get back to the detector, it would simply go through the less dense material and carry on. Real X-Ray machines work by firing X-Rays from an emitter on one side at a plate on the other, with bones and other dense structures showing up because they do not allow the rays to pass through; the traditional X-Ray with white bones is a negative, showing where the rays did not pass through, not where they were reflected back at the emitter. The net result is that the scope wouldn't actually display anything at all unless the entire area was saturated with lethal radiation or an emitter were present on the opposite side of the target.
Desert Eagle
U.S. Marshall John Kruger (Arnold Schwarzenegger) steals a Desert Eagle off of another deputy during the plane shootout and keeps it until the zoo shootout when he runs out of bullets, conveniently having 2 bullets left(as opposed to the 40 or so he fires before without reloading) to shoot out the crocodile glass exhibit, and shoot an approaching crocodile remarking, "You're luggage."
Beretta 92FS
Deputy Monroe (Danny Nucci) uses a Beretta 92FS as his personal sidearm for his duration in the film. Kruger uses one akimbo with his Glock 17 at one point in the film. A few unnamed thugs use 92FSs as well.
U.S. Marshal Robert Deguerin (James Caan) reveals his true colors by killing a woman with a dead assassin's Beretta 92SB, as noted by its briefly seen rounded trigger guard.
Glock 17
U.S. Marshall John Kruger (Arnold Schwarzenegger) uses a Glock 17 as his sidearm, swapping out the barrels from a regular Glock and the Glock 17 Pro barrel, threaded for a suppressor. He later steals one off of a man in the warehouse by the docks.
Olympic Arms OA-93 Pistol
One of the assassins in the woman's house is seen using an Olympic Arms OA-93 Pistol before being knocked out a window by Kruger.
Calico M951 Carbine
Cyrez security guards use Calico M951 carbine rifles.
Walther PPK/S
U.S. Marshal Robert Deguerin (James Caan) uses a Walther PPK/S as his sidearm and commonly threads a suppressor on it.
IMI Uzi
The Uzi is seen in the hands of several thugs throughout the film and is also used by U.S. Marshal Robert Deguerin (James Caan) and Johnny Casteleone (Robert Pastorelli).
A couple of thugs can be seen using MP5K submachine guns.
Smith & Wesson Model 38 "Bodyguard"
Kruger tells Lee Cullen (Vanessa Williams) that he works alone and if anyone ever says they are with him, to use his Smith & Wesson Model 38 "Bodyguard", a snub nosed Smith and Wesson revolver with a rounded hammer shroud to prevent clothing snag. It appears to use Harret grips, as they wrap aroud the shroud.
Kruger uses a Benelli M3 Super 90 shotgun with a top-folding stock while in the dock warehouse. When two snipers armed with Railguns destroy half the place, the bolt on his gun melts to the reciever, rendering it useless. He tosses it over to a thug searching for him, and he picks it up. A sniper sees him with the shotgun and remarks, "Nice shotgun, asshole." and blasts him instead.
Walther PPK
The men trying to kill Johnny and his wife during the beginning scene use older Walther PPKs. Kruger takes one of these for his own use, yet it changes into three guns, the suppressed PPK.....
Colt Woodsman
....A Colt Woodsman with an integral suppressor....
Heckler & Koch P7M13SD
...and an H&K P7M13SD, as noted by its added suppressor.
Remington 870
Deguerin uses a Sawed-off Remington 870 to blast the vault code pad. It is doubtful a high security vault would simply open by blasting the code pad, to add.
Drillbit Launcher
The scarred thug uses a custom built Drillbit Launcher, that appears to launch a weighted rubber grenade which after several seconds, launches a 'Bouncing Betty' mine into the air. The mine explodes and propels hundreds of pieces of barbed darts in all directions. One dart succeeds in impaling Kruger's hand to the fridge door.
Smith & Wesson 6906
Johnny Casteleone (Robert Pastorelli) takes a Smith & Wesson 6906 compact double action off a guard in Cyrez.
Winchester Model 70
Sal (John Snyder) uses a Winchester Model 70 with a scope to shoot out one of the EM snipers. He fires a bullet right through the scope, similair to the legendary USMC sniper Carlos Hathcock, who did the same thing with the same rifle during Vietnam.
AKM
Russians at the docks uses AKMs as noted by their open sights and slanted muzzle breaks.
M16A1 w/ A2 style handguard
U.S. Marshalls towards the end of the film are armed mainly with M16A1s with A2 style handguards as evident by its A1 style sights and standard barrel.
M16A2
Although one of the rifles does appear to have A2 style sights so this one is an M16A2, not just an M16A1 with A2 handguards.
Daewoo USAS-12
One of the U.S. Marshals is seen using a Daewoo USAS-12 full-auto assault shotgun with a 20 round drum magazine.