When Jason Bourne (Matt Damon) visits the bank in Zurich, he gets ahold of his safety deposit box and, inside, finds several passports, cash and a SIG Pro SP2009 pistol. Shortly thereafter, he takes the passports and money and leaves the gun in the box.
During the search for Bourne in the U.S. Embassy in Zurich, the Marine Staff Sergeant can be briefly seen with a Heckler & Koch MP5K. (This is a continuity error, as he was carrying an M16 variant in other shots).
U.S. Marines arm themselves with various M16/AR-15-model assault rifles when searching for Bourne in the U.S. Embassy in Zurich. Strangely, all of the rifles seen in this scene appear to be civilian AR-15 variants, many of which are clearly "post-ban" versions (if you look on the armory wall, you can see many lack flash hiders and bayonet lugs - all signs of the "politically correct" black rifles that used to be sold in American gun shops). The ones with the short barrels are Bushmaster "Dissipator" carbines, an AR-15 variant that used to be sold only to LE agencies, but is now available to civilians since the Assault Weapon Ban ended.
A U.S. Embassy worker carries a black SIG-Sauer P229, which Bourne manages to take from him during a struggle. Bourne tosses the gun in a trash can while making his escape.
Castel (Nicky Naude) has a Taurus PT945 in his case with his passports and money. He is never seen using it. One of the assassins in the Paris Treadstone safehouse also has a suppressed stainless PT945, which Bourne disarms him of. Bourne then fires the PT945 and Walther P5C akimbo, but the PT945 is upside down because he took it from the assassin very quickly and didn't have time to adjust his grip.
The Professor (Clive Owen) uses a SIG SG 550 Sniper as his weapon of choice, assassinating Nykwana Wombosi (Adewale Akinnuoye-Agbaje) in Paris with it. He is seen with the rifle again later in the French countryside, after he tracks down Jason Bourne and Marie Kreutz to Marie's stepbrother's home.
Jason Bourne (Matt Damon) uses an unidentified 12 Gauge Double Barreled Shotgun belonging to Eamon (Tim Duttin) to search for and shoot the Professor, after the Professor tracks him and Marie to the farmhouse in the French countryside. It appears to be a hammerless, box lock action, side by side shotgun with a Churchill or Uplander stock and a splinter fore end. No other details can be made out.
Jason Bourne carries a Walther P5 Compact in the Treadstone safe house in Paris after taking it from the Professor (Clive Owen). After disarming an assassin with armed a suppressed Taurus PT945, Bourne uniquely carries the P5C and the PT945 akimbo.
I don't think Conklin's gun was a P5C. It looked like something else, almost like a Walther PP, but I couldn't tell for sure. -MT2008
During the flashbacks to his mission to kill Wombosi (Adewale Akinnuoye-Agbaje), Jason Bourne (Matt Damon) is seen holding a Glock 19 fitted with a laser sight to Wombosi's head.
