A Swiss policeman carries a SIG P225, which Bourne swiftly disarms him of and expertly disassembles.
SIG P229
A U.S. Embassy worker carries a black SIG P229, which Bourne manages to take from him during a struggle. Bourne tosses the gun in a trash can while making his escape .One of the assassins in the Paris Treadstone safehouse also has a suppressed stainless SIG P229, which Bourne disarms him of. Bourne then fires the SIG P229 and Walther P5 akimbo, but the P229 is upside down.
SIG Pro SP2009
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.
Taurus PT92
Castel (Nicky Naude) has a Taurus PT92 in his case with his passports and money. He is never seen using it.
Walther P5 Compact
Jason Bourne carries a Walther P5 Compact in the Treadstone safe house in Paris. After disarming an assassin with a SIG P229, Bourne uniquely carries the P5 and the P229 akimbo. Conklin (Chris Cooper) also briefly carries one that he found in Nicky Parsons' (Julia Stiles) field kit.
Heckler & Koch MP5K
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. (A continuity error, as he was carrying an M16 variant in other shots).
Micro Galil
When Bourne is in his apartment, Castel (Nicky Naude) breaks through the window, firing a Micro Galil, to try and kill Bourne and Marie.
AR-15
U.S. Marines arm themselves with AR-15 rifles when searching for Bourne in the U.S. Embassy in Zurich.
All of them seem to be civilian AR-15 variants, many of them "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. -MT2008
SIG 550 Sniper
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.
unidentified side-by-side shotgun
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.