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 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.
Mock Grenade Launcher
When Cyrus takes the guns out of the weapons hold, a few of the cons use mocked up grenade launchers made to mimic the function of an M79 grenade launcher. Based on what is visible, it looks like a break open tube with a Smith & Wesson Model 15 revolver inside (note the hammer and double action function) the grip with a Smith & Wesson 4506 trigger guard. It is fitted with a wooden stock with a similair shape to an M79 as well.