The top 5 episodes that gave me the chills are:
1. The mysterious passenger, this episode gave me the chills because Haibara wasn't acting like her usual self that's what clued me in the first time that I saw it. Haibara is usually such a strong character and for her to act like a "child" that was unsettling for me. It also scared me because of Akai's scowl.
2. The moonlight sonata case, this episode scared the juice out of me. I am terrified of the moonlight sonata now. It still makes shivers race down my spine.
3. Dracula's Villa. I think the fact that they talk about Dracula and horror flicks in this episode and that they discussed Nosferatu was enough to get the blood rushing.
4. Jet Black Mystery Train. These few episodes sent shivers down my spine, I was terrified of how these episodes would end and how much drama could be pushed into so few episodes.
5. The Old Blue Castle. This last one scared me because of the old woman and how she refused to answer any questions.