I'm only up to episode 193, so I can't speak for later episodes; however, among those my favorites are - in no particular order:
Second Season (don't know episode name or number) - the doctor who gets the money and toys, and Ran almost figures out Conan's secret. LOVE the ending where she confronts him, and then Dr Agasa saves the day (and Conan's skin!).
34-35 Mountain Villa Murder Case - I LOVE when Ran is asleep next to Conan and he can't think because he's distracted by her mouth.
96 (et al) Caught Up with the Great Detective - it's neat seeing Ran almost figure things out with Conan. A great two-hour special.
129 The Girl from the Black Organization - nice addition to the world of Conan.
140 SOS Message from Ayumi - I like seeing an episode where the kids work things entirely on their own.
156 Metropolitan Police Detective Love Story - another neat use of the kids, and it's hilarious to see the entire police force racing to find the two missing officers as they think the suspect is hurting the lady cop. A bit sexist, yet still funny. And the addition of the bomb in the building adds to the tension.
188 (et al) the Desperate Revival series - Ran again close to discovering Conan's secret, a great kids' mystery in the cave, a close call for Conan, and then a great episode with Shinichi AND Conan together. THAT really caught me off guard!
Anyway, there's my input.