One of the guards at the parking garage entrance to the Merovingian's (Lambert Wilson) Club packs a two tone Beretta 92FS Brigadier, noted by its thickened slide near the ejection port. He attempts to kill the protagonists with it when they demand entrance, only for Trinity (Carrie-Anne Moss) to end up killing him with his own weapon.
Beretta 92FS Brigadier Inox
Once the protaganists have entered the Merovingian's (Lambert Wilson) Club, Trinity (Carrie-Anne Moss) begins a standoff by disarming one of the guards of their Beretta 92FS Brigadier Inox and holding it to the Merovingian's head, demanding Neo (Keanu Reeves) be freed from the train station.
Browning BDM
Seraph's (Collin Chou) weapons of choice are a pair of Browning BDM pistols. In the club, one of the guards holds one of his BDMs to his head.
Heckler and Koch P9S
During the standoff at the the Merovingian's (Lambert Wilson) Club, Morpheus can be seen with a Heckler & Koch P9S which he takes from one of the guards..
IMI Desert Eagle Mark XIX
One of the guards outside the Merovingian's (Lambert Wilson) club draws an IMI Desert Eagle Mark XIX on Seraph (Collin Chou) before being disarmed by him. The weapon appears again, quite briefly, in the hands of a Smith copy later in the film. This confirms a Desert Eagle has been used in all three Matrix films.
Colt Detective Special
The Trainman (Bruce Spence) can be seen armed with a 1st generation Colt Detective Special in the film, firing off way more shots than should be possible without reloading.
Glock 17
One of the Merovingian's (Lambert Wilson) guards uses a pair of Glock 17 pistols to shoot at the protaganists at the club entrance. One of the guards inside the club can also be seen holding a Glock 17 on Morpheus (Laurence Fishburne). The Glock is the third and final weapon to be used in all 3 film (Albeit, the one in Reloaded was an 18C)
Beretta 92FS
One of the guards at the entrance to the club wields a pair of full-sized Beretta 92FS pistols. One of the guards inside the club can also be seen holding one on Seraph.
Smith & Wesson 5906/5904 (Two-tone)
One of the guards outside the club wields a pair of two-tone pistols which based on their shapes are Smith & Wesson 5906 pistol frames with Smith & Wesson 5904 slides.
Morpheus (Laurence Fishburne) uses a pair of Heckler & Koch MP5K's with the foregrips removed exposing the barrels therefore making them more like "machine pistols", as well as being fitted with M68 Aimpoint red dot scopes. This is yet another weapon seen in all three Matrix movies, albeit not in this exact configuration.
Heckler & Koch UMP-9
One of the Merovingian's (Lambert Wilson) guards uses a Heckler & Koch UMP-9 with the folding stock removed during the shootout at the club entrance, noted as the 9x19mm version by its curved magazine.
Shotguns
Ithaca 37
The muzzle of an Ithaca 37 shotgun is seen trained on Trinity (Carrie-Anne Moss) during the standoff in the club.
Mossberg 590
One of the guards in the club aims a Mossberg 590 with a heat shield and ghost ring sights.
Remington 870 Sawed Off
One of the guards in the club is seen aiming a sawed down Remington 870 with raised barrel ribbing.
Rifles
FN FNC-80 Para
One of the guards in the club is seen using an FN FNC-80 Para fitted with an A1-style birdcage muzzle brake. The gun appears to be the same one used by Al Pacino in Heat, or at least a very close copy.
Armory
When the protaganists first exit the elevator on the club room floor, the guards are seen manning a station in front of a wall armory. Most of the guns on the wall are difficult to see, but some can be made out.