The EM-1 Railgun (EM standing for "Electro Magnetic"), a fictional railgun, is the film's prominent weapon. The weapon is described as being able to fire aluminum 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.
Handguns
Glock 17
Deputy U.S. Marshal John Kruger (Arnold Schwarzenegger) carries a Glock 17 as his sidearm, sometimes swapping out the barrel from a regular Glock for a Glock 17 Pro barrel threaded for a suppressor. He later steals one from a man in the warehouse by the docks. Like the Beretta, it is also used by several thugs in this movie.
Beretta 92FS
Both Deputy Marshal Calderon (Nick Chinlund) and Deputy Marshal Monroe (Danny Nucci) carry the Beretta 92FS as their sidearm. Kruger dual-wields a Beretta along with his Glock 17 at one point in the film. J-Scar (Mark Rolston) uses the 92FS as well. During the final gunfight, Tony Two-Toes (Joe Viterelli) also carries the weapon.
In an apparent continuity error, US Marshal Robert Deguerin (James Caan) picks up a dead assassin's Beretta 92SB as noted by its briefly-seen rounded trigger guard, which was previously seen as a Beretta 92FS.
High Standard Sharpshooter M
Kruger also is seen using what appears to be a suppressed .22 cal High Standard Sharpshooter M with wooden grips.
Desert Eagle
Kruger (Arnold Schwarzenegger) steals a Desert Eagle Mark XIX from Agent Schiff (Michael Papajohn) during the plane shootout and keeps it until the zoo shootout when he runs out of ammunition, conveniently having 2 rounds 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!"
Heckler & Koch P7M13SD
Kruger uses an H&K P7M13SD, as noted by its added suppressor.
Smith & Wesson Model 36 (Lightning Grips)
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 36. It appears that this is a regular Model 36 with Bianchi "Lightning" grips that give the gun a "Bodyguard" appearance.
The hitmen sent to kill Johnny Casteleone (Robert Pastorelli) and his wife at the film's beginning use older Walther PPK pistols. Kruger takes one of these for his own use, yet it changes into three guns, the suppressed PPK.
Walther PPK/S
Deputy Marshal Robert Deguerin (James Caan) uses a Walther PPK/S as his sidearm and commonly threads a suppressor on it.
Submachine Guns
Calico M951 Carbine
Cyrez security guards carry the Calico M951 carbine rifle as their main weapon. These appeared to be fitted with scopes and laser sights.
One of the thugs that pursue Lee and Kruger into the reptile house is armed with a Heckler & Koch MP5K.
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).
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.
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 receiver, rendering it useless. He tosses it over to a thug searching for him, and he picks it up. A railgun sniper spots the thug with the shotgun and blasts him instead.
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.
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.
Rifles
AKM
Russians at the docks uses AKMs as noted by their open sights and slanted muzzle brakes.
Custom AKMS
An AKMS with a chopped barrel is also used by one of the Russians at the dock.
M16A1 (w/ A2 style handguard)
U.S. Marshals towards the end of the film are armed mainly with M16A1s with A2 style handguards as evidenced by their A1 style sights and standard barrels.
M16A2
At least one of the U.S. Marshals has an actual M16A2 rifle, rather than just an M16A1 with A2 handguards as this particular rifle does appear to have A2 style sights.
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, similar to the legendary USMC sniper Carlos Hathcock, who did the same thing with the same rifle during Vietnam.
Other
Drillbit Launcher
J-Scar (Mark Rolston) uses a custom built Drillbit Launcher, that appears to launch a weighted projectile which after several seconds, launches a grenade vertically into the air. The grenade then explodes and propels hundreds of drillbit-shaped fragments in all directions. One succeeds in impaling Kruger's hand to the fridge door.