A Beretta 92FS with a suppressor is seen in "The Indiscriminate Threatening Stadium Case (Part 2)" with Hiruta, masquerading as a Nichiuri TV cameraman.
The Kel-Tec P-11 is seen in "The Girl from the Black Organization and the University Professor Murder Case" with the forger known as Silver Fox. Ai Haibara aka Shiho Miyano uses it to scare the living daylights out of her.
The M1911A1 is seen, strangely, with Tokyo Metropolitan Police officers in the season. Most of the TMPD never use semi-automatics except for specialized units like the Special Investigation/Assault Team or the Security Police. While the M1911A1 has a history of use in Japan, only the Japanese Self-Defense Forces has a record of using them as the Allied Forces provided the pistols until they changed to the Minebea P9. It's seen used by a bald villain in a TV action drama Conan was watching in "A Mysterious Sniper Murder Case (Part 1)". In "The Girl from the Black Organization and the University Professor Murder Case", Conan uses a discarded M1911A1 to kick it at Silver Fox and disarm her of her P-11.
A Walther PPK/S is used in "The Black Organization: 1 Billion Yen Robbery Case" by Hirota Masami aka Akemi Miyano before she meets with Gin and Vodka at a deserted warehouse.
A Nambu Model 60 appears to be seen in a next episode preview eyecatch in "The Naniwa Serial Murder Case". This is contrast with the first season, where such an eyecatch showed the exact same weapon.
A Smith & Wesson Model 29 is seen in "A Mysterious Sniper Murder Case (Part 1)" as a murder weapon uncovered after Shiro Hiraoka, a criminal trying to blackmail chairman Seiji Ishimoto of the Ishimoto Company, was unmasked as the initial suspect. It's also used by a white jacket-wearing character in an action drama Conan was watching. In "A Mysterious Sniper Murder Case (Part 2)". Sergeant Takagi finds it rigged to a stage lamp.
A Smith & Wesson Model 36 is seen throughout "Masked Yaiba Murder Case" as a key piece of evidence Conan use to pin Osamu Honda as the murder suspect. Katsuji Mishima also uses it to shoot Osamu.
A Smith & Wesson Model 66 is used by Osaka Prefectural Police officer Yusuke Sakata aka Yusuke Inaba as his sidearm in "The Naniwa Serial Murder Case".
Error creating thumbnail: File missingThe green jacket-wearing character aims the revolver in "A Mysterious Sniper Murder Case (Part 1)". It's a continuity error since he was using a M1911A1. There's not enough details to give a good ID.
Others
Bowgun
A bowgun is seen in a next episode preview eyecatch in "Magic Lover's Murder Case (The Murder)". It's seen in "Magic Lover's Murder Case (The Suspicion)" and "Magic Lover's Murder Case (The Resolution)".
