Policemen and FBI agents are seen with Beretta 92FS pistols in "Sleight of Hand" (S1E10). Michael Scofield (Wentworth Miller) and Fernando Sucre (Amaury Nolasco) are seen with this weapon in season 4. Don Self (Michael Rapaport) also uses one briefly in "Selfless".
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.
Browning Hi-Power
In season 2, Brad Bellick (Wade Williams) holds a Browning Hi-Power on Lincoln, Michael and Nika. When they escape, Lincoln takes the pistol from him. The pistol is briefly taken from Lincoln by Nika (Holly Valance) when she decides to turn them in, but Lincoln reveals that he took the magazine out and put it in his pocket.
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. John Abruzzi (Peter Stormare) also uses a nickel plated version this pistol in season 2, when he goes to assassinate Fibbonachi. Lincoln Burrows (Dominic Purcell) carries this pistol as his sidearm for most of season 3. Michael Schofield (Wentworth Miller) also briefly handles Lincoln's 1911 to try and shoot Gretchen in the season 3 finale. T-Bag (Robert Knepper) used this pistol in season 4. Also wielded by Homeland Security Agent Herb Stanton (Michael O'Neill) in "Deal or No Deal."
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).
This is possibly the most common weapon seen throughout season 4. Characters including Donald Self (Michael Rapaport) uses this as a sidearm.
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).
Alexander Mahone (William Fichtner ) carried a 2nd generation as his service sidearm during Season 2. Christina Scofield (Kathleen Quinlan) uses one in season 4 along with Trishanne (Shannon Lucio).
Heckler & Koch P7M13
William Kim (Reggie Lee) carries a Heckler & Koch P7M13 fitted with a suppressor as his sidearm for most of season 2. it is kept in a cross draw shoulder holster.
Heckler & Koch USP Compact
Paul Kellerman (Paul Adelstein) uses this pistol throughout season 2.
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.
SIG-Sauer P226
Seen as one of the pistols Wyatt (Cress Williams) carries in season 4.
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).
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.
Alex Mahone (William Fichtner) is given a Smith & Wesson 5906 by his ex-wife, and uses it as his sidearm for several of the episodes in season 4.
Walther PPK
James Whistler (Chris Vance) used a Walther PPK .380 in the premiere of Season 4. In season 2, Mahone (William Fichtner) uses this pistol as his back up gun.
A guard is seen with an MP5A3 while escorting Link to meet his son in "Bluff" (S1E18).
Heckler & Koch MP5K
A Heckler & Koch MP5K fitted with an extended barrel is used by a Company Agent in the "Sona".
Heckler & Koch MP5SD
Gretchen uses a Heckler & Koch MP5SD while holding the GATE office hostage in "Selfless". In the episode, despite being a trained killer, she inexpertly sprays from the hip rather than shoulder the weapon when shooting at the employee.
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.
Company Agent uses a scoped Ruger Mini-14 in the "S.O.B.".
Shotguns
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), when they capture the escaping Sanchez.
Remington 870
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)
Remington 700 AICS
Mahone uses a Remington 700 AICS fitted with a Harris bipod in Season 4. SWAT Snipers used these rifles during the prison riot during Season 1.
Other
CS Grenade
Multiple number of CS grenades are used by guards during a fight between prisoners in "Allen" (S1E02).