A Beretta 92FS with a suppressor is seen in "The Indiscriminate Threatening Stadium Case (Part 2)" with Hiruta, masquerading as a Nichiuri TV cameraman.
Colt Commander
What seems to be a stainless Colt Commander is used by Masao Kouda in "The Mysterious Mole Alien Case (Part 2)"
Glock Full-Size
A Glock-based full-size pistol is seen as a light gun-type controller in an arcade parlor in "A Mysterious Sniper Murder Case (Part 1)".
Kel-Tec P-11
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 Miyanao uses it to scare the living daylights out of her.
M1911A1
The M1911A1 is seen, strangely, with plainclothes 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)".
TT-33
The Tokarev TT-33 is seen in "The Indiscriminate Threatening Stadium Case (Part 1)".
Walther P38
The Walther P38 is seen with a TV villain in an action drama Conan was watching in "A Mysterious Sniper Murder Case (Part 1)".
Walther PPK/S
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.
Revolvers
Nambu Model 60
A Nambu Model 60 appears to be seen in a next episode preview eyecatch in "The Naninwa Serial Murder Case". This is contrast with the first season, where such an eyecatch showed the exact same weapon.
Smith & Wesson Model 19
A Smith & Wesson Model 19 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.
Smith & Wesson Model 36
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.
Smith & Wesson Model 66
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". It also appears to be used by Hiraoka in "A Mysterious Sniper Murder Case (Part 1)".
Unknown Revolver
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)".