Canadian Policemen and FBI agents are seen with Beretta 92FS pistols in "Sleight of Hand" (S1E10). Prison Guards are also seen with Berettas in "Flight" (S1E22).
Beretta 92FS Inox Non Gun
In "Sleight of Hand" (S1E10), one of Abruzzi's goons uses a Beretta 92FS Inox Non Gun to kill two men in a flashback.
Glock 17
Michael Scofield (Wentworth Miller) carries a Generation 2 Glock 17 during the bank robbery in order to get himself incarcerated into Fox River in "Pilot" (S1E01).
Glock 19
Special Agent Daniel Hale (Danny McCarthy) carries a Generation 2 Glock 19 pistol during the first season. He uses it to shoot the escaping Leticia in the leg in Season 1's "Cell Test" (S1E03), and to kill LJ's mother "The Old Head" (S1E08). Bellick (Wade Williams) retrieves a Glock 19 from his safe but he never uses it in "Riots, Drills and the Devil: Part 1" (S1E06). One of Abruzzi's men kills Nick and his father with a Glock 19 in "Go" (S1E21).
IWI Jericho 941 R
Philly Falzone (Al Sapienza) is seen chambering a Jericho 941 R pistol when the hit squad arrives to Fibonacci's home in "Sleight of Hand" (S1E10). The slide mounted safety can be seen for a brief second when he exits the car. Maggio (Rich Komenich) is seen with a Jericho pistol in "Flight" (S1E22) when the Air Strip Controller walks to their plane.
M1911A1
Veronica spots an M1911A1 pistol in a cabinet while she is searching for coffee at Nick's father's safehouse in "Tweener" (S1E09). In "And Then There Were 7" (S1E11), Quinn (Michael Gaston) shoots Nick with an M1911A1.
SIG-Sauer P226 (Two-Tone)
In "End of the Tunnel" (S1E13), Spider (Eric Lane) is seen with a Two-Tone P226 for a brief time when two guards approach Darius' car in front of the Fox River prison.
SIG-Sauer P228
Special Agent Paul Kellerman (Paul Adelstein) carries a SIG-Sauer P228 during the first season. He uses a suppressed P228 to kill Adrian Rix, LJ's step father in "The Old Head" (S1E08).
Ruger KP89
In "Allen" (S1E02), Lincoln (Dominic Purcell) is seen using a Ruger KP89 in flashback. (This flashback is seen again in "Brother's Keeper" (S1E16), without the blur effect.) In "Cute Poison" (S1E04), another flashback has Lincoln checking out two similar Ruger KP89 pistols at Bo's place.
A guard is seen with an MP5A3 while escorting Link to meet his son in "Bluff" (S1E18).
Assault Rifles
AR-15
In "Pilot" (S1E01), a guard at the prison fires an unknown AR-15 at the fighting prisoners. The rifle is fitted with a scope and fixed stock.
M4A1 Carbine
In "Allen" (S1E02), a Fox River prison guard is seen patrolling with an M4A1 Carbine when Michael meets T-Bag at the yard. M4A1's are also seen during the riot. Benjamin Miles "C-Note" Franklin (Rockmond Dunbar) is seen with an M4A1 in a flashback to his US Army days in Iraq in "Brother's Keeper" (S1E16).
M16A2 Rifle
In "Riots, Drills and the Devil: Part 2" (S1E07), soldiers and prison guards are seen with M16A2 rifles during the riot.
Shotguns
Ithaca 37
Brad Bellick (Wade Williams) is seen with a pistol-gripped Ithaca 37 shotgun in "Flight" (S1E22).
Mossberg 500 Persuader
Numerous Mossberg 500 Persuader shotguns are seen at the prison armory when the guards are responding to the riot in "Riots, Drills and the Devil: Part 1" (S1E06). Corrections Officer Keith Stolte (Christian Stolte) points a Mossberg 500 at Michael and the others when they enter a restricted area in "The Old Head" (S1E08). In "The Key" (S1E19), Bellick (Wade Williams) is holding a Mossberg 500 when he is apprehending Lincoln. Several guards are armed with Mossbergs in "Go" (S1E21) and "Flight" (S1E22), when they capture the escaping Sanchez.
Sniper Rifles
Remington 700PSS
Soldiers responding to the prison riot are seen with Remington 700PSS rifles with adjustable butt-plates in "Riots, Drills and the Devil: Part 2" (S1E07)
Other
CS Grenade
Multiple number of CS grenades are used by guards during a fight between prisoners in "Allen" (S1E02).