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 appears to be the primary weapon of Roy Miller in this movie.
SIG-Sauer P228
A suppressed SIG-Sauer P228 is pulled by one of the men who confront Miller on the plane. Miller then disarms the man, and uses the gun briefly.
Heckler & Koch USP Expert
One of the agents (the pilot) on the plane tries to pull a Heckler & Koch USP Expert, fires at Miller which accidentally kills another agent. The pilot is shot and killed and accidentally shoots his co-pilot.
Roy gives June a 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.
Heckler & Koch G36C
One of Fitzgerald's men uses a Heckler & Koch G36C during the tunnel firefight. It's also used by covert operatives when chasing Roy on the roof.
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 tranport 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.