Neo (Keanu Reeves) opens up with a GE M134 Minigun mounted on a Bell 212 helicopter while rescuing Morpheus. According to armorer John Bowring, they were firing the gun half-speed at 3,000rpm though the gun was capable of firing 6,000rpm.
Glock 17
In the opening scene police burst in on Trinity (Carrie-Anne Moss) with Glock 17 pistols drawn. These are 3rd Generation models, which were pretty new at the time the film was shot (1998).
Trinity (Carrie-Anne Moss) carries a pair of Beretta 84FS Cheetahs as her sidearms in the film. These were selected because Ms. Moss has small hands and full sized Beretta 92Fs would be gigantic in her hands. What is interesting to note is that besides the Micro Uzi used in the beginning of the lobby scene, this is the only gun that Trinity feels she needs to bring into a building guarded by three agents. Meanwhile, Neo packs about a dozen guns and a bomb.
Zastava CZ99
Apoc (Julian Arahanga) gives Neo (Keanu Reeves) his Zastava CZ99 pistol as they try and escape an Agent-led SWAT attack after visiting the Oracle. The weapon is a CZ99 and not, as has been written previously, a SIG-Sauer P228; some of the weapons rental invoice documents published on Propstore.com have confirmed this. The CZ99 is a Yugoslavian-made pistol which is based on the P220 series, but is actually a very different weapon.
Beretta 92FS
Neo (Keanu Reeves) takes at least four pairs of Beretta 92FS pistols with him on his mission to save Morpheus (Laurence Fishburne), because for some reason he sees more logic in carrying eight pistols instead of just one or two with spare magazines to reload.
M16 (SP1)
In the lobby shootout scene where Neo and Trinity encounter the security guard's "back-up" in the form of a unit of soldiers, the majority of the soldiers Neo and Trinity face up against are armed with M16 (SP1) rifles with slab-side receivers. The M16s used in this scene are a mixture of rifles with 3-prong flash hiders and rifles with M16A1-style "birdcage" flash hiders. Neo uses two of these M16s during this scene, one while cartwheeling across the lobby, another while on the roof.
Micro Uzi
During the lobby scene, Neo and Trinity both use Micro Uzis, Trinity using one to kill one of the first guards and Neo using two to keep the soldiers behind cover.
Cobray M11/9
Apoc (Julian Arahanga) carries a Cobray M11/9 converted to full-auto with a thread protector, and is famously seen firing it to lay down cover fire while he and the others are fleeing from the SWAT team (you can tell it's a Cobray M11/9 and not an original Ingram MAC-10 because the back of the receiver is elongated).
Heckler & Koch MP5K
In the lobby scene, Neo uses a pair of Heckler & Koch MP5Ks to eliminate the first set of guards.
Mouse's Shotguns
Mouse's (Matt Doran) pair of shotguns are custom-built cam-operated electric driven automatic 12 gauge shotguns with 25-shell cylinders and a fire rate of 900 rounds per minute. They were crafted by John Bowring, lead armorer of the film. As an inside joke, Bowring named the guns "Andy" (serial no. A1169 - Leetspeak for Andy) and "Larry" (serial no. L2779 - Leetspeak for Larry) after the Wachowski brothers, the writers and directors of the film. It can be assumed in the movie world, Mouse designed these shotguns for himself like he designed the woman in the red dress.
Franchi SPAS-12
In the lobby shootout scene, a number of soldiers are armed with Franchi SPAS-12 shotguns, some of which are commandeered and used against their original owners by Trinity. The versions used by the soldiers have a solid fixed stock/pistol grip combination.
Goof: One soldier can be seen using the SPAS-12 on semi-auto -- a rare sight in movies. However, quick bursts of M16 fire are mistakenly dubbed over instead of an appropriate shotgun report.
Leader Dynamics T2 MK5
The SWAT team that breaks into the apartment building during the "deja vu" scene are armed with Australian-made Leader Dynamics T2 MK5 assault rifles (the Semi automatic version known as the SAC). (although the weapons are never shown clearly on screen, this has been confirmed by the rental invoices from Propstore, which also has one of the rubber AAA carbines on sale). The T2 Mk5 is loosely based on the Armalite AR-18 and was planned to be the next service rifle of the Australian Army, but the rifle lost out to the Steyr AUG during the Australian Army's service rifle trials. The versions used in The Matrix are the "Commando" version which have 11.5-inch barrels; the weapons are also fitted with large tactical flashlights and laser sights. The use of an Australian weapon in this case makes sense, as most of this was filmed in Sydney, Australia.
Skorpion SA Vz 61
Neo fires a pair of Skorpion SA Vz 61 submachine guns fitted with muzzle shrouds and 30 round magazines during the lobby shootout.
Browning Hi-Power
Switch (Belinda McClory) is seen carrying a silver chrome Browning Hi-Power with adjustable sights in 9mm caliber as her weapon of choice, first holding Neo at gunpoint with it while Trinity removes the "bug" the Agents planted in him, then using it to lay down cover fire along with Apoc while the others escaped the SWAT team, taking out several SWAT members in the process.