The first episode they appear in is episode 1, in which two members clad in black (later found out to have the code names Gin and Vodka), shrink Shinichi. After episode 1, they, along with members Vermouth, Chianti, Korn, Calvados, Sherry (Haibara), Pisco, Tequilla, Kir (Hidemi Hondou), Akemi, and others appear in:
128 The Black Organization 1 Billion Yen Robbery Case
129 The Girl from the Black Organization and the University Professor Murder Case
176 Meeting With the Black Organization Again (Haibara)
177 Meeting With the Black Organization Again (Conan)
178 Meeting With the Black Organization Again (Resolution)
309 Contact With the Black Organization: Negotiation Chapter
310 Contact With the Black Organization: Pursuit Chapter
311 Contact With the Black Organization: Desperation Chapter
345 part 1 Head-to-Head Match With the Black Organization; Two Mysteries of the Night of the Full Moon
345 part 2 Head-to-Head Match With the Black Organization; Two Mysteries of the Night of the Full Moon
425 Black Impact! The Moment the Black Organization Reaches Out!
462 Shadow of the Black Organization: The Young Witness
463 Shadow of the Black Organization: The Strange Illumination
464 Shadow of the Black Organization: The Mystery of the Big Reward
465 Shadow of the Black Organization: The Pearl Shining Star
491-504 Clash of Red and Black
Also, they have been in 2 movies; movie 5 (countdown to heaven) and movie 13 (the raven chaser)
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Episodes 501-504
48,49,57,58,77,78,117,118,141,142,166,167,168,174,189,190,191,219,221,222,223,224,238,239,240,263,277,278,291,292,293,323,324,325,326,327,345,381,382,283,406,407,408, 479, 484, 490, 491,515,516,517,521,522,523,554,555 OVAs 1,2,3,6,9 Movies 3,7,10,13, and 14 (As of July 15, 2010)
episode 130/131 the stadium indiscriminate threatening case.
he appeared in ep.509, he's a graduate student, he also posses an exceptional deductive and observational skills, it is believed by conan and sherry that he is one of the new members of the black organisation: Bourbon, who is also said to be a very intelligent, comparable to sherlock holmes
The best detective conan site would be gogoanime.com. It is good for anime on the whole.