The Company Agent sent to eliminate Lincoln carries a 92FS in "Scylla" (S4E01). Link (Dominic Purcell) takes his gun and shoots the Agent with it in the same episode. Feng's bodyguards are also carrying Berettas in "Quiet Riot" (S4E11). Fernando Sucre (Amaury Nolasco) holds a 92FS on General Krantz and his bodyguard in "Selfless" (S4E12). In "Deal or No Deal" (S4E13), Sucre holds a 92FS on Sooter.
Gretchen (Jodi Lyn O'Keefe) holds a Colt Mustang on General Krantz in "Greatness Achieved" (S4E09). In "Selfless" (S4E12), she tries to kill T-Bag with the Mustang.
Glock 17
Wyatt (Cress Williams) uses a suppressed Glock 17 in "Scylla" (S4E01). In "Shut Down" (S4E03), Wyatt kills Bruce Bennett with his Glock 17. ICE Homeland Security Investigations Special Agent Donald "Don" Self (Michael Rapaport) carries a Glock 17 as his service weapon; most notably in episodes "Eagles and Angels" (S4E04), "Quiet Riot" (S4E11), and "Deal or No Deal" (S4E13). General Krantz (Leon Russom) holds a Glock 17 on Gretchen in "Quiet Riot" (S4E11). Sooter (Kirk B.R. Woller) has a Glock 17 in "Deal or No Deal" (S4E13). Lincoln uses Sooter's Glock in the same episode.
Glock 19
Michael (Wentworth Miller) threatens to kill Gretchen with a Glock 19 pistol in "Scylla" (S4E01). In a flashback, Gretchen (Jodi Lyn O'Keefe) holds a Glock 19 in "Breaking and Entering" (S4E02). Clozza (Dylan Kenin) holds a suppressed Glock 19 on Lincoln in "Eagles and Angels" (S4E04).
Miriam Holtz (Shannon Lucio) uses a Glock 26 while saving the hostages in "Selfless" (S4E12).
Kahr K9
In "Blow Out" (S4E06), Gretchen (Jodi Lyn O'Keefe) retrieves a Kahr K9 from her sister's house. Later in the same episode, she confronts T-Bag with the Kahr.
M1911A1
An M1911A1 is wielded by Homeland Security Agent Herb Stanton (Michael O'Neill) in "Deal or No Deal" (S4E13).
SIG-Sauer P226
Wyatt (Cress Williams) is seen assembling a SIG-Sauer P226 in "The Price" (S4E08). When he shoots Roland, the P226 becomes a Non Gun (see below). Lincoln (Dominic Purcell) holds a P226 on General Krantz in "Selfless" (S4E12).
SIG-Sauer P220 Series Non Gun
Wyatt (Cress Williams) "kills" Gretchen with a SIG-Sauer P22X Non Gun in "Scylla" (S4E01). In "The Price" (S4E08), Wyatt shoots Roland with a Non SIG three times.
SIG-Sauer P232
Feng Huan (Ron Yuan) threatens T-Bag with a SIG-Sauer P232 pistol in "Safe and Sound" (S4E05) and "The Price" (S4E08).
Alexander Mahone (William Fichtner) is given a Smith & Wesson 5906 by his ex-wife in "Safe and Sound" (S4E05), and uses it as his sidearm for several episodes in Season 4. Mahone is seen with the 5906 twice in "Five the Hard Way" (S4E07). He also uses it in "Selfless" (S4E12).
Some of General Krantz' bodyguards carry MP5A3 submachine guns in "Selfless" (S4E12).
Heckler & Koch MP5K
Vikan's bodyguards carry Heckler & Koch MP5K submachine guns with Navy trigger groups in "Deal or No Deal" (S4E13).
Heckler & Koch MP5SD3
Gretchen (Jodi Lyn O'Keefe) uses a Heckler & Koch MP5SD3 with Navy trigger group while holding the GATE office hostage in "Selfless" (S4E12). In the episode, despite being a trained killer, she inexpertly sprays from the hip rather than shoulder the weapon when shooting at the employee.
T-Bag (Robert Knepper) uses a suppressed Heckler & Koch G36C while holding the GATE office building hostage in "Selfless" (S4E12). Later Gretchen refers to the rifle as "MP5".
Company Agent uses a scoped Ruger Mini-14 in "S.O.B.".
Shotguns
Remington 870
Lincoln's sidekick uses a Remington 870 shotgun in a flashback in "The Price" (S4E08). The 870 is fitted with a pistol-grip and low-cap tubular magazine.
Sniper Rifles
Remington 700 AICS
Mahone uses a Remington 700 AICS fitted with a Harris bipod in Season 4.