Not sure if this is all but here u go :)
48-49 Diplomat Murder Case (1-2)
57-58 Holmes Freak Murder Case (1-2)
96 Caught Up With the Great Detective! 2 Murder Cases!
129 The Girl from the Black Organization and the universiteit Professor Murder Case
176-178 Meeting With the Black Organization Again
188-193 The Desperate Revival
226-227 The Battle Game Trap (1-2)
230-231 The Mysterious Passenger (1-2)
258-259 The Man from Chicago (1-2)
271-272 The Secret Rushed Omission (1-2)
277-278 English Teacher vs. Western Detective (1-2)
284-285 Chinatown Deja Vu (1-2)
286-288 Shinichi Kudo's New York Case (1-3)
307-308 The Dark Footprint (1-2)
309-311 Contact with the Black Organization (1-3)
345 Confrontation with the Black Organization
425 When the Black Organization Reaches out
429-430 The People Who Cannot Return (1-2)
446-447 The Sealed Western-Style Window (1-2)
462-465 The Shadow of the Black Organization
479 Three Days With Heiji Hattori
484-485 The Whereabouts of the Black Photograph (1-2)
491-504 Clash of Red and Black
507-511 Various episodes
521-523 Various episodes
u can also check this website -
link in the character appearances xD