Fox River guards chasing Michael and the others are seen with Beretta 92FS pistols in "Manhunt" (S2E01). Coyote (José Zúñiga) puts a 92FS to Michael's head in "Bolshoi Booze" (S2E11). Later Michael (Wentworth Miller) takes the Beretta from him. T-Bag (Robert Knepper) carries a Beretta 92FS in "Fin del camino" (S2E21). A company agent carries a 92FS in "Sona" (S2E22), which is later taken by Link and Michael.
In "First Down" (S2E04) 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. Link holds his HP on T-Bag in "Map 1213" (S2E05).
Glock 17
In "Scan" (S2E03), a cop is seen with a Glock 17 when he stops Sucre's car. In "Map 1213", (S2E05), a Glock 17 is seen in Alex Mahone's (William Fichtner) pants, even though he is carrying a Glock 19 as his service weapon in the other episodes.
Glock 19
FBI Agent Alexander Mahone (William Fichtner) carries a 2nd Generation Glock 19 as his service sidearm during Season 2. In a continuity error in "Buried" (S2E07), a P226 changes into a Glock 19. Sara (Sarah Wayne Callies) takes Mahone's Glock 19 in "Sweet Caroline" (S2E19).
Heckler & Koch P7M13
Special Agent William "Bill" Kim (Reggie Lee) carries a Heckler & Koch P7M13 fitted with a suppressor as his sidearm during Season 2. It is kept in a cross draw shoulder holster. He is seen with it in "Bad Blood" (S2E17), "Sweet Caroline" (S2E19), and "Sona" (S2E22).
Heckler & Koch USP Compact
Paul Kellerman (Paul Adelstein) switches to a Heckler & Koch USP Compact pistol when Lincoln takes his P226. He is seen using the USP Compact in "John Doe" (S2E14), "The Message" (S2E15), "Chicago" (S2E16), and "Bad Blood" (S2E17).
M1911A1
Sucre (Amaury Nolasco) shoots Coyote with an M1911A1 pistol in "Bolshoi Booze" (S2E11). Aldo Burrows (Tony Denison) takes the pistol from Sucre and fires at Mahone in "Disconnect" (S2E12). A robber (Channon Roe) holds an M1911A1 on C-Note and the others in "Chicago" (S2E16). Paul Kellerman (Paul Adelstein) tries to commit suicide with an M1911A1 in "Fin del camino" (S2E21). His pistol eventually jams when he fires it.
M1911A1 (Nickel)
John Abruzzi (Peter Stormare) uses a nickel plated M1911A1 pistol in "First Down" (S2E04), when he goes to assassinate Fibbonachi.
Ruger KP89
A flashback to the first season shows Lincoln (Dominic Purcell) using a Ruger KP89 in "Sona" (S2E22).
SIG-Sauer P226
The SIG-Sauer P226 is the most seen pistol in Season 2. Ann Owens (Alexandra Lydon) pulls out a SIG-Sauer P226 in "Buried" (S2E07). Later Sucre (Amaury Nolasco) uses the P226 when he betrays his partners and leaves with the cash. Paul Kellerman (Paul Adelstein) carries a suppressed P226 in "Rendezvous" (S2E10) and "Disconnect" (S2E12). Alexander Mahone's Glock 19 changes to a P226 in "Bolshoi Booze" (S2E11). Link (Dominic Purcell) and Steadman (Jeff Perry) are seen with Kellerman's P226 in "John Doe" (S2E14). Bellick (Wade Williams) receives a P226 from Mahone in "Chicago" (S2E16). He is seen with it when he is chasing Haywire later in the same episode. Michael (Wentworth Miller) is seen with Lincoln's (or Kellerman's if you wish) P226 in "Bad Blood" (S2E17). In "Panama" (S2E20), Sucre (Amaury Nolasco) takes Bellick's P226 and tries to persuade him to let him go. In "Fin del camino" (S2E21), Sucre, Bellick and Michael are seen with the same P226.
SIG-Sauer P226 (Nickel)
Roy Geary (Matt DeCaro) is seen with a nickel P226 in "First Down" (S2E04). Agent Blondie (Steven Chester Prince) tries to kill Sarah with a nickel P226 in "Dead Fall" (S2E08).
SIG-Sauer P226 (Two-Tone)
In "Sona" (S2E22) one of DeJesus' bodyguards holds a Two-Tone P226 on Michael.
SIG-Sauer P220 Series Non Gun
Agent Blondie (Steven Chester Prince) uses a SIG-Sauer P22X Non Gun to kill Veronica in "Manhunt" (S2E01). One of Kim's men uses a Non Gun SIG-Sauer to kill two men guarding Lincoln and his son in "Bolshoi Booze" (S2E11). Kellerman (Paul Adelstein) shoots Mahone with a Non Gun SIG-Sauer pistol in "The Killing Box" (S2E13). In "Wash" (S2E18), Kellerman buys a Remington 700 sniper rifle with a Choate Ultimate Sniper Stock, and then kills the seller with a Non Gun SIG-Sauer. It is not explained how did he get a SIG-Sauer, as his P226 is now in Lincoln's possession.
Walther PPK
During Season 2, FBI Agent Alexander Mahone (William Fichtner) uses a Walther PPK pistol as his backup gun, most notably in "Buried" (S2E07).
Revolvers
Colt Python
In "John Doe" (S2E14), Susan Hollander tries to take out a 4" Colt Python revolver from a drawer when T-Bag visits her. Later in the same episode, T-Bag (Robert Knepper) is seen holding the same Python.
Brad Bellick (Wade Williams) is seen with a pistol-gripped Ithaca 37 shotgun in "Manhunt" (S2E01) when searching for the fugitives. He tries to use his Ithaca to commit suicide in "Otis" (S2E02).
Mossberg 500 Persuader
Fox River guards chasing the fugitives are carrying Mossberg 500 Persuader shotguns in "Manhunt" (S2E01). In "The Killing Box" (S2E13), Persuaders are seen in the hands of US Border Patrol. Police officers are seen with Mossbergs in "Chicago" (S2E16).
Serbu Super Shorty
Two hit men sent to eliminate Kellerman are using Serbu Super Shorty shotguns in "Sona" (S2E22).
Submachine Guns
Heckler & Koch MP5K
A Heckler & Koch MP5K fitted with an extended barrel and SEF trigger pack is used by a Company agent in "Sona" (S2E22).
Assault Rifles
AR-15 Variant
Police officers at the motel use unknown AR-15 variants in "First Down" (S2E04).
M16 Variant
Two Mexican police officers are seen holding unknown M16 variants in "The Message" (S2E15).
M16A2
Panamanian police officers are seen with M16A2's in "Fin del camino" (S2E21).
M4A1
Several Panamanian policemen chasing Michael and Sara are armed with M4A1 carbines in "Sona" (S2E22).
Sniper Rifles
Remington 700 (Choate Ultimate Sniper Stock)
In "Wash" (S2E18), Kellerman (Paul Adelstein) buys a Remington 700 sniper rifle with a Choate Ultimate Sniper Stock. In the next episode, "Sweet Caroline" (S2E19), he plans to assassinate the President Caroline Reynolds, but eventually decides not to pull the trigger.
Unknown Sniper Rifle
Kellerman (Paul Adelstein) plans to shoot Michael and Lincoln with an unknown sniper rifle in "The Killing Box" (S2E13). This weapon is never fired in the episode.
Other
Water Gun
In "Otis" (S2E02), Lincoln (Dominic Purcell) threatens Mahone with a water gun. Michael paints the water gun black to pass for a real pocket pistol.
X26 Taser
In "Sweet Caroline" (S2E19), Brad Bellick (Wade Williams) holds an X26 Taser on Sucre. The X26 has a yellow finish and is fitted with an XDPM (Extended Digital Power Magazine). There is no cartridge inserted, but the X26 can be still used in "drive stun" mode.