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.
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..
Glock 26
Aimed at Morpheus in the club by one of the armed guards.
Walther PPK
One can be seen pointed at Trinitys head.
Colt Detective Special
During the standoff at the the Merovingian's (Lambert Wilson) Club, The TrainMan (Bruce Spence) can be seen armed with an early-generation Colt Detective Special which he points at Seraph's (Collin Chou) head. He also fires it at the protagonists as they're chasing him through the subway station earlier in the film.
Kahr K9
Right in the front someone is seen pointing this at Morpheus' back.
It looks like a Kahr K9. And what did I say about writing properly on the site? - Gunmaster45