The SIG-Sauer P226, with accessory rails is the sidearm of U.S. Deputy Marshals Charlie Duchamp (Laz Alonso) and Ray Zancanelli (Domenick Lombardozzi). Several criminals also use the P226.
Glock 17
The Glock 17 appears as the sidearm of various law enforcement personnel and criminals. One is also used by Damien Fontleroy.
Glock 17 (Converted to Full Auto)
Vega cartel gunman use Glock 17s converted to full-auto when they assasinate an informant and the US. Marshals with him in "Where in the World is Carmen Vega" (S1E13)
Glock 26
In "Fun with Chemistry (S1E7) Charlie hands Erica his backup gun, a Glock 26, when they clear a building. Carmen Vega uses a Glock 26 durign the events of "Where in the World is Carman Vega" (S1E13)
In "Paid In Full" (S1E10) a hitman, Virgil Downing, carries a suppressed Walther P22 as he avenges a rape victim, Genevieve Krause (Marcella Lentz-Pope).
Walther P88
A Vega cartel gunman holds a Walther P88 pistol on Vanessa, Shea's girlfriend, in "Where in the World Is Carmen Vega" (S1E13)
M1911A1
In "Round Two" (S2E2), Brody Ardell (James Harvey Ward), an undercover FBI agent, is given an M1911A1 by the Victor Mannion (Channon Roe), a fellow escape .
Beretta 92FS Inox
Ronald Barnes carries a Beretta 92FS Inox in "There are Rules" (S1E12). Victor Mannion carries a Beretta 92FS Inox in "Round Two" (S2E2) as well.
Smith & Wesson Model 686
In the Season 1 Pilot eppisode, and again in "Fun with Chemistry" (S1E7), the escaped convicts can be seen using a Smith & Wesson Model 686 with a 3-inch barrel.
Submachine Guns
Mini Uzi
A Vega cartel gunman fires a Mini Uzi during the assault on Flo-Flo's strip club. Due to the (lack of) lighting, it is impossible to determine exact model, but it is most probably a Mini model
Shotguns
Remington 870
In Queen of Hearts(S1E5), Deputy US Marshal Ray Zancanelli is seen with a Remington 870 shotgun with synthetic furniture. Several criminals and prison guards are seen wth the weapon in later episodes.
Ithaca 37
In the episode "An Unjust Death", a man meets Damien Fontleroy at the door of his house armed with an Ithaca 37 shotgun, Damien later takes it for his own use.
Mossberg 590
In the episode "An Unjust Death", a prison guard can be seen armed with a Mossberg 590 shotgun with a high-capacity magazine tube when Damien Fontleroy breaks out of prison.
Rifles
Ruger Mini-14
In "Like Father, Like Son" (S1E6) Christian Beaumont (Zack Ward), an anti-government extremist, opens fire on the Breakout Kings with a Ruger Mini-14 when they raid his bunker.
AR-15 A2 HBAR
In the episode "An Unjust Death", another prison guard can be seen carrying an AR-15 A2 HBAR when responding to Damien Fontleroy's jailbreak.
M16A4 Rifle
An M16A4 rifle are carried by prison guards in various episodes.
Type 56-1
In "There Are Rules" (S1E12), the break-in driver uses a Norinco Type 56-1 with a drum magazine to cover the escapees
Other
DefTech 37mm launcher
A prison guard in "One for the Money" (S1E9) uses a DefTech 37mm launcher to fire a tear gas round during a riot.
12 Gauge Orion Flare Gun
In "There Are Rules" (S1E12), Ray uses an Orion Flare Gun found on a boat to disable Ronald Barnes (Jeff Seymour) with a shot to the leg.