Jason Bourne (Matt Damon) has a Beretta 92SB at the beginning of the movie when he and Marie (Franka Potente) are escaping from Kirill in Goa, India. He is shown pulling one out of the glovebox of the SUV (suzuki samurai) they are in.
After Marie is killed in India, Jason Bourne (Matt Damon) packs his Beretta 92F up with his belongings when clearing out of their former home. Jarda (Martin Csokas), another ex-Treadstone agent, also carries a Beretta.
Jason Bourne (Matt Damon) uses a SIG-Sauer P225 throughout the movie after arriving in Naples, stolen from U.S. Consulate agent John Nevins (Tim Griffin). It is most notably seen when he confronts Treadstone asset Jarda in his home, and when Bourne uses it to shoot through the door of his stolen taxi at Kirill's Mercedes in Moscow. Bourne also used a P225 in his flashback to the Neski double-murder (his first assignment).
The FSB assassin Kirill (Karl Urban) uses a 1st generation Walther P99 with a QPQ finished slide during his pursuit of Jason Bourne. It is most notably seen in his hands when he wounds Bourne from an overhead bridge while in Moscow, and later during the film's final car chase when fired from Kirill's Mercedes towards Bourne's taxi. There is also a publicity photo of Bourne using a standard black first-gen P99, though no scene in the movie depicts this.
Maybe in a deleted scene-GunnutHk
Several of the German SWAT team officers who attempt to arrest Bourne at the hotel are armed with what appear to be Heckler & Koch G36 rifles. However, a close inspection of the rifles reveals that they are actually the civilian SL8 version, except visually modified to resemble G36s by adding 30-round magazines and regular G36 carry handles.
Jason Bourne (Matt Damon) uses a bolt-action, bullpup sniper rifle when talking to Pam Landy (Joan Allen) at the CIA headquarters in Berlin. The rifle may be a Keppeler & Fritz KS II precision rifle that's been given a custom scope mount and a suppressor (http://www.bullpup.de/repetier/ks2/), but this is highly uncertain. The scope looks to be a Zeiss, but the rifle itself may actually have been custom-built specially for the movie by a good gunsmith.
