Fox River guards chasing Michael and the others are seen with Beretta 92FS pistols in "manhunt" (S2E01).
Browning Hi-Power
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
In a continuity error in "Buried" (S2E07), a P226 changes into a Glock 19. Alexander Mahone (William Fichtner) carries a 2nd Generation Glock 19 as his service sidearm during 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.
Heckler & Koch USP Compact
Paul Kellerman (Paul Adelstein) uses this pistol throughout Season 2.
M1911A1 (Nickel)
John Abruzzi (Peter Stormare) uses a nickel plated M1911A1 pistol in "First Down" (S2E04), when he goes to assassinate Fibbonachi.
SIG-Sauer P226
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.
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).
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).
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.