S1E01: Michael Scofield (Wentworth Miller) carries a Generation 2 Glock 17 during the bank robbery in order to get himself incarcerated into Fox River.
This is possibly the most common weapon seen throughout season 4. Characters including Donald Self (Michael Rapaport) uses this as a sidearm.
Glock 19
S1E03: Special Agent Daniel Hale (Danny McCarthy) uses a Generation 2 Glock 19 pistol to shoot the escaping Leticia in the leg. S1E08: Special Agent Hale kills LJ's mother with a suppressed Glock 19.
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).
SIG-Sauer P226
Seen as one of the pistols Wyatt (Cress Williams) carries in season 4.
SIG-Sauer P228
S1E08: Special Agent Paul Kellerman (Paul Adelstein) uses a suppressed SIG-Sauer P228 to kill Adrian Rix (LJ's step father).
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.
Heckler & Koch USP Compact
Paul Kellerman (Paul Adelstein) uses this pistol throughout season 2.
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.
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.
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.
Colt 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."
Ruger KP89
S1E02: Lincoln (Dominic Purcell) is seen using a Ruger KP89 in flashback. S1E04: In another flashback, Lincoln is seen checking out two similar Ruger KP89 pistols at Bo's place.
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
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
S1E02: A Fox River prison guard is seen patrolling with an M4A1 Carbine when Michael meets T-Bag at the yard.
M16A2 Rifle
S1E07: Soldiers and prison guards are seen with M16A2 rifles during the riot.