My FAVOURITE episode of all time is "The Trembling Police Headquarters: 12 Million Hostages" (ep. 304). Great case, clever code, great tension, the coolness of Matsuda, and the Takagi x Sato-ness I cannot emphasise how much I love this episode!
I also like cases with Shinichi in them (flashback or reverting back), the Metropolitan Police Love Stories (especially Takagi x Sato), cases where Kogoro is actually a competent detective, and "The Culprit is Genta's Dad" (ep. 551-552) (Genta's dad is great!)