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 Brigdaier 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 Stainless Inox model Beretta 92FS Brigadier 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.
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 scopes.
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
Even though it isn't seen in the hands of any Agents, 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. This confirms a Desert Eagle has been used in all three Matrix films.
One of the Merovingian's (Lambert Wilson) guards uses a Heckler & Koch UMP-9 during the shootout at the club entrance, noted as the 9mm version by its curved magazine.
^Why do all of the Merovingian's guards look like S&M freaks? - Gunmaster45
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).
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 (Collin Chou).
Smith & Wesson 5906/5904 tutone
One of the guards outside the club wields a pair of tutone pistols which based on their shapes are Smith & Wesson 5906 pistol frames with Smith & Wesson 5904 slides.
This was all I could match, so if anyone has a suggestion it would be appreciated. - Gunmaster45