Jason Bourne (Matt Damon) uses a SIG Pro SP2022 in Moscow when he is accosted by the Russian police in a pharmacy. He later has one in New York, seen "Mexican-carried" in his waist. This interchanges with a Glock when he is questioning Dr. Hirsch about his past. Neal Daniels (Colin Stinton), CIA station chief in Madrid, takes a SIG Pro when he goes on the run. One of the CIA agents sent in "heavy" to Daniels' office in Madrid has a SIG Pro with a camera attached. Bourne beats him up and takes it.
Glock 19
The CIA agents pursuing Bourne in London and Madrid carry Glock 19 pistols. An NYPD officer carries a Glock 19 as well.
Beretta 92FS
One of the CIA agents attempting to apprehend Simon Ross at Waterloo Station has a Beretta 92FS. Jason Bourne (Matt Damon) takes one from a Tangier police officer when chasing Desh in Morocco.
The CIA agents in New York, including Noah Vosen (David Stratharn) and Pamela Landy (Joan Allen), carry Glock 17s. Jason Bourne (Matt Damon) also carries a Glock in New York City. Bourne's flashbacks to joining the Treadstone program show him with a Glock 17. Many NSA agents also use the Glock including the agents who capture the guy in the blue hood. The agents that hunt Bourne down in Sewell & Marbury. Bourne then takes one of the Glocks and then uses it to threaten Nikki. It often changes into a Sig Pro while threatening Nikki too.