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.
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 M16A3 prop
When Cyrus throws down his empty M16A3, it changes to a rubber prop featturing the M16A2 style sights but lacking a forward assist and shell deflector.
U.S Marshal Vince Larkin (John Cusack) uses a Glock 17 2nd generation as his issued sidearm.
Defense Technologies 1315 37mm
When Cyrus 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.
Suppressed Pistol
One of the Cartel members uses an unknown pistol with an extended barrel to thread a suppressor and target style grips. Cameron Poe (Nicholas Cage) comment that the cons would hear the shot, so he threads a suppressor on it. When Poe disspatches all the Cartel members, he takes the gun for his own use, before dropping it diving from an explosion. It actually resembles the LWS-32 from earlier in the film and could be a SD model or something. It also looks a bit like a Colt Woodsman pistol.