The prison guards U.S. Marshals and DEA agents arm themselves with SIG-Sauer P226 handguns. The convicts use several P226s captured from the guards, most notabley Cyrus "The Virus" Grissom (John Malkovich), who steals the co-pilot's SIG-Sauer from him after he removed it from the lock box.
Remington 870
Prison guards carry Remington 870s when the Cons are being loaded on the plane.
M16A3
The cons take several M16A3 assault rifles from the weapons stash. While they could be M16A3s, the full auto version of the M16A2, they are most likely M16A2 upper recievers, placed on full-auto lower recievers, or genuine M16A2s with drop in full-auto auto sears.
Rubber M16 prop
When Cyrus throws down his empty M16A3, it changes to a rubber prop featturing the M16A1 style sights and lacking a forward assist, shell deflector, and magazine fencing. It could have possibly been cast from an AR-15/SP1 rifle.
M16A1 (With A2 handguards)
The national guardsmen and some of the prison guards are armed with M16A1 rifles fitted with M16A2 handguards.
Skorpion SA
A cartel member (Eddie Pérez) duel wields two guns, one being a Skorpion SA, the other being..
Beretta 92SB
...a Beretta 92SB pistol, noted by its rounded trigger guard.
Seecamp LWS-32
The undercover DEA agent Willie Sims (José Zuñiga) is given an LWS-32 .32 ACP pistol, which he draws before being killed by Cyrus.
Glock 17
U.S Marshal Vince Larkin (John Cusack) uses a Glock 17 2nd generation as his issued sidearm.
Defense Technologies 1315 37mm
When Cyrus (John Malkovich) takes the guns out of the weapons hold, a few of the cons use Def Tech 1315 37mm launchers, used to look like HE launchers.
Colt Woodsman "Assassin" Model
One of the cartel members (Thomas Rosales Jr) uses a Colt Woodsman with a modified barrel to thread a suppressor, commonly known as the "Assassin" model. Cameron Poe (Nicolas Cage) comments that the cons would hear the shot, so he threads a suppressor on it. When Poe dispatches all the cartel members, he takes the gun for his own use, before dropping it diving from an explosion.