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.