Baja California police officers Javier Rodriguez (Benicio del Toro) and Manolo Sanchez (Jacob Vargas) each carry a Colt Mk IV Series 70 1911. The two cartel men that take Javier and Manolo out into the desert later also carry Series 70s (possibly the policemen's own pistols).
M16A2
Several of Salazar's soldiers carry M16A2 assault rifles.
I think these are M16A1s with A2 handguards. The one in the third picture is, at least (it has the A1-style rear sight). -MT2008
Heckler & Koch MP5A3
Some of Ruiz's drug smugglers use Heckler & Koch MP5A3 submachine guns during the battle with the San Diego PD and the DEA.
Heckler & Koch USP Tactical
Eduardo Ruiz (Miguel Ferrer) draws a Heckler & Koch USP Tactical and shoots DEA Agent Gordon in the chest. Gordon pulls the slug out of his bulletproof vest once Ruiz leaves the room.
Note the point trigger guard and the shape of the slide. It's actually a Mark 23. -MT2008
unidentified pistol
One of Ruiz's henchmen, shot by Castro, carries a small silver pistol.
Glock 17
DEA Agent Ray Castro (Luis Guzman) carries a Glock 17 as his standard sidearm. Several other DEA agents and San Diego police carry and use them during the shootout outside Ruiz's office.
Minor mistake, but the Glock 17s in the movie are the 2nd Generation models, so you shouldn't use the picture of the Gen 3 Glock 17 to illustrate the gun. -MT2008
DEA agents towards the end of the film carry M16A1 assault rifles.
M16A1s with A2 handguards. Probably the same guns used by the Mexicans, being reused in another scene. This should be merged with the entry above. -MT2008
unidentified suppressed pistol
The hitmen sent by Carlos Ayala (Steven Bauer) to assassinate Arnie Metzger (Dennis Quaid) are seen entering his office with a small suppressed pistol