After getting used to Aoyama thwarting kisses and otherwise making romance in Detective Conan proceed only a little more quickly than a glacier for over a decade, file 673 offered a genuine treat for fans. Takagi is hospital-bound after his drubbing by the killer. Satou—with whom Takagi got two or three (depending on whether you go by manga or anime) Almost Kisses—is at his side, and Takagi is resigned to the two of them getting interrupted yet again. Sure enough, it looks like Megure, Chiba, and Shiratori are about to enter his room to check up on him, but the Detective Club intervenes, claiming (at Satou's behest?) that Takagi is sleeping off his medication, so he should not be awakened. After Megure & Co. depart, the kids open the door a crack to check on how Takagi is doing. Next half-page-sized frame: Satou leaning over Takagi, the two of them in one very happy kiss.
They get another one in chapter 808. Takagi has just spent two days kidnapped, at threat of hanging, and nearly blown up. Satou saves his life, and they share a kiss. Doubles as a Crowning Moment of Funny due to the event being broadcast by webcam to the whole department.
Conan's favorite soccer player is arrested. Heiji ends up cheering him up, and the girls comment the two are like brothers.
There's an episode when Shinichi's parents show up, tell him (after an episode-long test of his detective skills that nearly gave him a heart attack SEVERAL times) that they know he's stuck in a little boy's body, and they still love him and he has their approval to keep fighting crime and looking for the evil organization on his own. Oh, and they're proud of him.
Another moment comes from Ayumi realizing Ai Haibara is the only friend she calls by her last name, and spending the arc trying to get up the nerve to call Haibara by her first name. The arc ends with Haibara having realized this and giving Ayumi permission to be on a First Name Basis. Also combines with Funny Moments since she immediately shoots down the boys' request before they can even get the question out.
Chapters 548 and 549 featured the kids' teacher, Kobayashi, giving her students a rainy day activity. She "mysteriously vanishes" and leaves clues for the kids to deduce her hiding place with. She even goes so far as to have Conan called out of class so he doesn't solve it too quickly. The story's end reveals Kobayashi deliberately took two students, a girl who had just transferred there and a boy who had been away for medical reasons, and made their names vital to solving the riddles with the ultimate aim of integrating these two students into the class and making sure nobody would forget their names.
The Mermaids episode. Kazuha decides to sacrifice her life so Heiji will live by stabbing his hand with the arrow she won while hanging from a cliff. But, Heiji still holds on and tells Kazuha not to let go.
A filler episode includes a girl named Haruna, whose parents are exactly the same as Ran's. Haruna wants her parents to come back but they don't get the hint until:
"Haven't you realised yet? Think of Haruna-chan's feelings after she took the Rainbow Child. Haruna-chan was lonely, her mom left her for a long time and her dad works nonstop everyday. That's when she thought of combining two sculptures into one, thinking this would bring back her family, just like the stork that would bring happiness."
The sea snake case during volume 17. You could clearly see that the character Harumi, the "villain" for that case, didn't really want to have done it and regretted it afterward, seeing as how, during the time that Conan was revealing the scheme piece by piece, she never even attempted to deny anything or tell him, "Well what about...?" The whole time she simply let him continue along, all the while looking almost sad and disappointed in herself. Once she admits to why she did it, even if she said at first that Kiwako probably deserved it, she begins crying at this point, telling you that even SHE doesn't believe that and that she hates having done it. Then, when Kiwako recovers and she goes there to apologize for what she did, it is instead Kiwako who apologizes for not having realized Harumi's feelings. Harumi practically killed her out of jealousy, but Kiwako just takes it in stride and accepts what happened as karma. It's no wonder Harumi practically admits her crime and begins crying again. And from what we're aware, Kiwako simply keeps it a secret, which means that Harumi totally escaped going to prison simply because of her kindness.
The anime rendition of this case (episodes 114 and 115, "Scuba Diving Murder Case") is just as beautiful.
In addition, this case is also a great example of showing how much Conan has matured as a human being, not just as a detective. He recognizes early (as does Eri) that it was an attempted murder, but doesn't shout out this fact to everyone in earshot (as he often does), and when it's time to confront Harumi, he does it with just Eri and Ran present, no cops, none of the other suspects. He learned his lesson from the Moonlight Sonata case, and here treats it as a human case, not just as a complicated puzzle to be solved.
Speaking of the Moonlight Sonata case: the villain who left his home island as a boy to return as a girl so he could get revenge sets the music hall on fire after Conan realises the truth: Conan follows to try to stop her. The murderer, who is touched by Conan's word, proceeds to save his life by throwing him out the window so the young detective doesn't burn alive.
In the 2nd Movie: The Fourteenth Target, Ran learns the real reason Eri divorced her father - she made him a thank-you dinner after he saved her life, and he yelled at her, telling her that if that was the best she could cook, she should go to bed. It was actually his way of showing he cared; she'd been injured and he wanted her to rest up instead of cooking!
Earlier in the movie, Kogoro asks how Conan got a cell phone call from the criminal, when Shinichi was supposedly the one on the case. Conan covers by saying that Shinichi left the phone the criminal would contact with him, and Kogoro is angry that Shinchi left the phone with a kid (putting said kid in danger), instead of with an adult.
At the end of episode 200, Kogorou admits that he misses Eri and asks her to come back, not knowing that she had earphones in and couldn't hear him. Later we find out she was listening and in fact recording what he said and plays it over and over to herself saying, "Not yet, for something like that", while blushing.
In the first movie, The Time Bombed Skyscraper, Ran spends the whole film talking about how she feels that she and Shinichi are connected by a red string of fate. During the climax, Ran has to disarm a bomb, but doesn't know whether to cut the red wire or blue wire. Conan realizes that the man who made the bomb knew that Ran's favorite color was red, and thus rigged the bomb to explode when she chose that color. In the end, Ran chooses the blue wire and the bomb doesn't go off. When Conan asks why she didn't pick the red wire, she alludes to not wanting to cut the red string between herself and Shinichi. Awww!
At the end of the last episode of the live-action series, Ran expects Shinichi to be angry with her, since she drugged him and her father on the villain's orders. Shinichi knows that she only did it because the villain was holding Eri hostage though, and assures Ran he isn't angry. The two are so sweet together that even Kogoro is moved to tears and excuses himself from the room. Even more adorable, the excuse he uses to leave? He's going to check on Eri, whose location they got out of the villain.
A minor one, but in a case from volume 73, as Conan deducts who the culprit is, his friends keep on defending him until he confesses himself. It's a little heartwarming, really.