The Beretta 34 was carried and used by Kirika Yuumura throughout the series, with and without its removable silencer. Noir is notable for its attention to detail during the sequences in which Kirika is cleaning her disassembled Beretta. Kirika's Beretta is usually carried in her pocket or waistband, rather than a holster. Chloe briefly takes and uses Kirika's Beretta in order to deliver to her 'the last guidance'. Altena later returns it.
Walther P99
The Walther P99 was used by Mireille Bouquet throughout the series, with and without its removable silencer. Like Kirika's Beretta, Mireille's Walther is shown in unusual detail in scenes where she has disassembled the gun for maintenance. Mireille usually carries her Walther in her handbag.
SIG Pro 2340
The SIG Pro 2340 is used by the majority of Soldat's Assassins as well as other enemies.
Desert Eagle Mk XIX
Pierre Cressoit, the leader of the French extreme nationalist faction, carries a Desert Eagle. It appears to be a .50AE model.
According to the notes in the DVD production sketches, it's a .44 Magnum model. Pravda616 But it doesn't show the fluted barrel common on the .44 TrueFork
Christian Gare, an old enemy of Mireille's, carries an early model CZ 75.
Walther P5
Mireille's uncle Claude uses a Walther P5, with removable silencer.
SIG P210
A high ranking Soldat's member sent to pass a message to Mireille and Kirika in Taiwan carries a SIG P210.
Makarov PM
The Triad members who attempt to trap Kirika and Mireille in Taiwan arm themselves with Makarov PMs. Kirika also uses one briefly in tandem with her Beretta 34.
Beretta 92F
The Knights of Paris mostly use Beretta 92fs equipped with silencers to attack Kirika and Mireille at their apartment.
The SPAS-12 is used by the Gleone family assassin named Paolo.
Rifles
M16 A1
The M16 A1 is used by the Ulgian Army when they are sent to kill Kirika and Mireille, and subsequently by Kirika to kill them.
AK-47
The Kalashnikov AK-47 is used by the revolutionary army and the Islamic revolutionary force whose leader is assassinated by Kirika in the unidentified desert country. One is also carried by a soldier in Altena's childhood flashbacks.
Heckler & Koch G36
The Troops who attack the Soldat's village in the Pyrenees are armed with Heckler & Koch G36s.
A Corsican assassin snipes with a scoped IOF.30-06 Sporting Rifle. This man later uses a SIG Pro 2340 as well.
Others
PanzerFaust III
The troops attacking the Soldats' village are seen carrying (a Panzerfaust III) recoilless anti-tank weapon, which they later fire at the church tower.
M26 Hand Grenade
The Taiwan Triad members use an M26 Hand Grenade against Kirika.
Unknowns
Margaret's shotgun
Margaret uses a double-barreled shotgun in episode 22.
Submachine gun
An East German hitman fires an unidentified submachine gun at Chloe. It might be another MAC-10.