Roy Miller (Tom Cruise) uses a two-tone SIG-Sauer P250 fitted with a laser sight as he rides the hood of a car driven by June Havens. He also uses dual full-sized SIG P250 without laser sights in the Spain shootout. This weapon is the primary sidearm of Roy Miller throughout the whole movie.
SIG-Sauer P229
Some of the agents who confront Roy Miller on the plane are armed with SIG-Sauer P229s. They are all suppressed. Miller also picks up one of the guns and uses it briefly.
SIG-Sauer P226
Federal Agent Fitzgerald's (Peter Sarsgaard) sidearm throughout the whole film is a nickel-plated SIG-Sauer P226. He most notably wields it during the climax.
Heckler & Koch USP Expert
One of the agents on the plane posing as the pilot tries to pull a Heckler & Koch USP Expert on Miller. But Miller shoots him and the pilot accidentally shoot his co-pilot.
Glock 19
Roy Miller (Tom Cruise) also keeps a Glock 19 on him. He most notably wields it when he takes June hostage. Miller also gives the Glock to June (Cameron Diaz) for protection just before the warehouse shootout.
Roy (Tom Cruise) uses the Taurus near the end of the freeway shootout. Roy later gives June the Taurus Judge, but she abandons it in a mailbox without using it.
Beretta 92G Elite II
Antonio Quintana (Jordi Mollà) uses a two-tone Beretta 92G Elite II in Spain. This particular Beretta has rails. Although it's appereance is brief, it is clearly a Beretta Elite, based on the cocking serrations, and the fact that it says "II" on the slide.
CZ 75 Automatic
During the warehouse shootout, one of the operatives is armed with a CZ 75 Automatic.
One of Antonio's men is seen firing a Heckler & Koch MP5A3 at Roy and June in Spain.
Heckler & Koch G36C
One of Fitzgerald's men uses a Heckler & Koch G36C during the tunnel firefight. It's also used by covert operatives and agents in the hotel and during the ensuing chase on the roof.
Heckler & Koch G36K
One of the agents that raid Roy's hotel room in Austria is seen holding a Heckler & Koch G36K.
Z-M LR 300ML
Roy uses a Z-M LR 300 ML during the tunnel firefight. He takes the weapon from the trunk of the car that the agents use when they try to transport June to 'safety'. The particular rifle is a carbine version of the full-sized rifle (Z-M LR 300). For anyone wondering what the magazines are, they are Magpul Pmags.
SIG SG 552
An agent is armed with a SIG SG 552 during the hotel raid.
Colt M4A1
One of the federal agents that are escorting Simon Feck in the hotel in Austria has an M4A1 assault rifle.