A Swiss policeman carries a SIG-Sauer P225, of which Bourne swiftly disarms him and disassembles. The Swiss (and German) Police used the SIG-Sauer P225 but the pistol was called the P6.
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 in most states since the Assault Weapon Ban ended. One Marine is seen obviously with a Rocky Mountain Arms Patriot Pistol (done up as a short carbine), and another Marine obviously has a C7 Style AR15 (i.e. the brass deflector, but A1 Rear Sight).
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 blued 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 side-by-side, 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, side by side shotgun with a box lock action and a Churchill or Uplander stock and a splinter fore end. No other details can be made out.
There are literally hundreds of "Boutique" gunmakers scattered across Europe. They often use parts (locks and triggers) made by larger companies such as FN or Beretta and then assemble them with stocks and barrels that they manufactured. This has been the norm in Europe for literally centuries. Unlikely the make of the shotgun will ever be determined.
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 armed with a suppressed Taurus PT945, Bourne uniquely carries the P5C and the PT945 side-by-side.
I was just taking those screens to help identify the above pistol and I discovered this shot of the second assassins pistol in that scene. It looks like a two tone Sig Sauer P226.
It could possibly be the same Sig they used earlier under different lighting.
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.
