I don't remember the ones that made me cry (if I did cry), but a lot of them made me want to cry :'(
28 - The one when Kogoro had to solve the case when his friend was murdered; it made me feel so proud of him
166 to 168 - Tottori spider mansion; I felt so bad for the murderer when he found out it was his fault his love killed herself
188 to 193 - The Desperate Revival Arc
304 - The Trembling Police Headquarters, everything was so intense
345 - The Halloween episode; when Ran stood up for Haibara and Vermouth didn't want to hurt Ran
491 to 504 - Clash of Red and Black Arc; best arc ever!
522 to 523 - When ran didn't want to let go of Shinichi <3
I know there's more, but these are some of the ones that came to mind