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 notably Cyrus "The Virus" Grissom (John Malkovich), who steals the co-pilot's SIG-Sauer from him after he removed it from the lock box and uses it for much of the film.
Beretta 92SB
A Beretta 92SB pistol is seen held by a cartel member, noted by its rounded trigger guard.
Colt Woodsman "Assassin" Model
One of the cartel members (Thomas Rosales Jr.) uses a Colt Woodsman with both a modified slide and 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.
Glock 17
Deputy US Marshal Vince Larkin (John Cusack) carries a Glock 17 2nd generation as his issued sidearm.
Seecamp LWS-32
The undercover DEA agent Willie Sims (José Zuñiga) is slipped a Seecamp LWS-32 .32 ACP pistol before boarding the plane, which he draws before being killed by Cyrus.
Shotguns
Remington 870
Corrections officers carry Remington 870s when the cons are being loaded onto the plane. Several 870s are also included in the arsenal located in the belly of the aircraft and are later broken out by the convicts.
Rifles
M16A2
The cons take several M16A2 assault rifles from the weapons stash. The rifles fire fully-automatic, which means that they are actually M16A2 upper receivers placed on full-auto lower M16A1 receivers, typical of all Hollywood "M16A2" rifles. This is even evident visually in some of the closeups.
Rubber M16 prop
When Cyrus throws down his empty M16A2, it changes to a rubber prop featuring the M16A1 style sights and lacking a forward assist, shell deflector, and magazine fencing. This means that the prop was mostly likely cast from a civilian AR15 Sporter-1 rifle fitted with A2-style handguards.
M16A1 (With A2 handguards)
The National Guardsmen, Deputy US Marshals, and Corrections officers are armed with M16A1 rifles fitted with M16A2 handguards. Actually these rifles are M16A1 barreled uppers with A2 handguards, however, the lower receivers are the original slab sided M16s.
Submachine Guns
Skorpion SA
A cartel member (Eddie Pérez) dual-wields a Skorpion SA alongside a Beretta 92SB in the hangar at the bone yard.
Other
Defense Technologies 1315 37mm
When Cyrus (John Malkovich) takes the guns out of the weapons hold, a few of the cons use DefTech 1315 37mm launchers, inaccurately portrayed as HE grenade launchers.