Hmmm... I think I can list three that I felt really sad or connected that I shed a tear or two.
1. Episode 193 when Conan told Ran that Shinichi went away on another case and Ran said she doesn't want to hear anymore excuses. Seeing her cover her ears and shout those words seem to pierce my heart.
2. Episode 345 when Ran went and hugged Haibara to protect her from Vermouth and Vermouth shouted 'Move it Angel!' Somehow even the darkest of hearts could be touched by one's selfless sacrifice.
3. Movie 4 when Sonoko watched over Ran and said even if her memory doesn't return, she will always be her friend. It reminded me of having best friends I can always count on.