The case of a certain Anti-Villain of the week in a (filler) case, "The Murder in the Mountain Villa!": he was the pupil and ghost writer for the Victim of the Week (a very eccentric murder mystery author who dressed up as a vampire) and said writer used to pay for his Ill Girl younger sister's hospital bills in exchange for the guy's hard work. We later learn the horrible truth: the poor girl actually died six months ago, because her older brother's boss actually bribed her doctor into keeping her on painkillers only instead of paying for crucial and expensive treatment abroad (as per his end of the bargain), so the brother could remain indefinitely as his subordinate, which ultimately killed her. And when the poor brother found out from the guilt-ridden nurse who used to tend to the girl, he went nuts with pain and murdered said boss. Asshole Victim seems a bit lenient. Conan himself lampshades the trope as he thinks "It's said that when a person is bitten by a vampire, they become vampires as well. He killed his boss and now is guilty. Poor guy! Revenge completely drained his body, mind, and soul..."
Seiji Asou aka Narumi Asai in Moonlight Sonata— the tear jerking part is not the motive rant on how he took revenge for his murdered family, but the fact that after that he decided to burn himself to death with his father's old piano, despite Conan's repeated appeals against that.
Ran's Broken Pedestal episode, "The Ski Lodge Murder", where the killer was her favorite teacher in elementary school, and she had to relay Conan/Shinichi's deductions (which he sent to her through a hidden microphone). Seeing Ran shake and cry as she "resolved" the case, with Conan mentally kicking himself as he tells her what happened... sniffff..
When Ran said "I wish you were Shinichi" at Conan's face, not knowing the truth about his identity. His reaction just makes it worse.
A number of the Poor Communication Kills examples are particularly tragic, especially when a misunderstanding leads to the death (sometimes at one's own hands) of a loved one. (Most notably the case where an American's written word "shine" is misread as "shi ne," or "die", causing his lover to kill herself, which leads him to go mad and kill her family.)
A girl rejecting her friend's confession because she knew that her other friend loved him.
The anime episode where Jerk AssIdol Singer Tatsuya Kimura is killed by his beautiful ex-girlfriend and manager, Mari Terahara, because of his verbal and mental abuse towards her. It's then revealed that Kimura was a Jerk Ass out of guilt because Mari got plastic surgery to be beautiful for him, but he loved her just the way she was before fixing her face.
The case involving Miyuki Hyuuga, a Sexy Secretary whose parents were killed by her boyfriend Hideomi (who came from the rich family that Miyuki was working for), when he was a teenager and she was only 6 years old, since he and his friend Mitsuaki caused the fire in which Miyuki's parents died. However, Hideomi felt guilty and returned for little Miyuki, saving her and becoming badly burned in the process.Ever since then, he helped raise her and encouraged her to live... while he himself lived with his sin. When Miyuki fell in love with Hideomi and asked him to marry her, he couldn't take it anymore and commited suicide out of guilt.. Then Miyuki became an accomplice to a plan by Mitsuaki, who wanted to kill Hideomi's dad/Miyuki's boss for power. Little did he know that Miyuki was planning to actually kill Mitsuaki too, since he also was involved in the incident in which she lost her family and she blamed him for Hideomi's death. Which she did.
Then, when Miyuki was unmasked, she took a pot supposedly filled with gasoline and got ready to burn herself to death. Then came her Motive Rant:
Miyuki: It's all as the detectives said! Everything about the fire was in the note. I couldn't forgive them! Mitsuaki, for being so carefree about it; Hideomi, for keeping it quiet for so long. But still... I loved him madly! Because he came back for me! And he always helped and encouraged me after losing my parents. And he even accepted to marry me! But Hideomi is gone. I'm alone again, so I have to go and to join him.
Then her suicide plan is botched (there was no gasoline, only water), and Miyuki breaks down even more. ("Why, why, why? His fire lit so easily, so why doesn't mine?!") Luckily, the chairman appeared and asked Miyuki to live for Hideomi, as her mother would've wanted her to. The chairman's first love turned out to be Miyuki's deceased mother.
And it's really not helped by Conan talking to Heiji, who had helped him resolve the case... and having flashbacks about the aforementioned Seiji Asou, whose death he considered as his greatest failure.
The case in which a lady named Kyouko Takahata killed her brother-in-law, Soejima, because she blamed him for the death of her older sister. It actually turned out that the sister had died... of illness, and that she and Soejima really loved each other. And by the time Kyouko heard her sister's phone message in which she told her how happy she had been in her married life, it was already too late.
In episode 605, the murderer the cameraman Mifune commit a crime for the sake of his girlfriend, an Idol Singer named Kira, whose murder was written off as an accident. The saddest part is that he killed the wrong person, a Kira fangirl named Shouko who had covered up for one of his previous murders. Shouko knew his part on it, and apparently threatened him with revealing it... and yet she loved him, but had to hide her love cause she knew he still loved poor Kira. She didn't offer any resistence when Mifune strangled her to death, thinking that she'd denounce him (when in fact she had decided to not do so), since being attacked by him made Shouko cross the Despair Event Horizon.
Also, made worse because a Cosplay Otaku Girl named Maho, also a Kira fangirl, reveals that she was present in the party where Kira died (Mifune thought it was Shouko)... and that she was heartbroken at Kira's death, since befriending Kira in Real Life helped Maho to get over the bullying that almost destroyed her life. And then, Maho tells the aforementioned truth about her fellow fangirl Shouko's love for Mifune.
Made even better/worse by the next episode... Where her now shrunk little sister Shiho aka Ai Haibara appears. It's not that bad until the end of the episode: except for one or two tears she kept her cool, but after the case of the day (the murder of Akemi's mentor, the real Masami Hirota) is resolved, Ai sorrofwully asks Conan why didn't he save Akemi when he had the chance and collapses in tears.
It was probably worse in the anime, where two versions of the episode exist. The case actually happened rather early on in the manga, and it was possibly the first one that actually had a sad and grim ending. Not aware of where this was going, the anime producers had Akemi survive. So, on watching it, you might probably think it's a mistake in the airing order... and then, wham, downer ending.
There were two Tear jerker cases coming right behind the other in season 5:
First, the "Great Writer's Disappearance Case" (episodes 116-117): The famous novelist Nitaro Shinmei and his wife have been missing for a while, apparently in retirement as he sends his scripts and novels to his editor via mail. Their daughter Kaori goes to Kogoro and Co. so they can decipher a series of strange code messages, which hint that the Shinmeis have actually been held hostage all the time. There never was a kidnapping, or even a crime. It was the very old and sickly Shinmei's Thanatos Gambit and last mystery, so he could die peacefully alongside his wife. In fact, when he's found, Shinmei is already dead of natural cases, and Mrs. Shinmei tearfully explains it all.
The "Naniwa Murder Case" (episodes 118 to 119): It was already hard to see Conan taking a knife to the gut for Ran and being saved only by an amulet that Heiji gave him, but the worst/better comes in the end... The Serial KillerSympathetic Murderer was Yusuke Sakata, a detective who worked with Kazuha and Heiji's fathers, and he did it out of revenge since 20 years ago, his father was killed via a prank by the Asshole Victims that went horribly wrong. Heiji finds out first (and he is appalled when he does, as is Conan a little later when he reaches the same conclusion) and goes confront Yusuke and make him turn himself in before he kills the last two targets and frames one of them for all of the murders. And then, to make things go From Bad to Worse... Yusuke pulls out his gun and tries to commit suicide, so he and Heiji struggle. Heiji manages to disarm Yusuke (and sets the warehouse they're in on fire as he empties the gun), but he has been shot in the stomach. Then comes the Motive Rant... followed by Heiji calling Yusuke a fool for using law as an element of revenge, then saving Sakata's life by helping him walk away from the fire. Really, really strong stuff, and not even the usually horrible Latin-American dub could kill the emotions.
From the Stranger In Ten Years OAV, one single phrase is enough to open the waterworks:
Older!Ran:"I've already waited ten years... so another ten will be just fine."
Older!Conan's flashbacks before he finally found her just makes it worse.
Arguably the whole of Stranger In Ten Years. It took me weeks to shake off the downer feelings it leaves behind.
The murder when a girl kills her sister, as we find out, for marrying the man she loved, despite her feelings. However as we quickly find out, it was actually the GUY who had pushed for marriage in the first place. She (the dead sister) told her (the killer) that before because she knew she'd be heartbroken if she knew the man she loved had fallen for her younger sister. She denies that her sister cared for her, until Richard (CONAN) reveals to her that she had gotten her certain chemicals (that she'd (the killer) PLANNED to use to kill her (the sister)) on purpose, knowing that it might cause a chemical reaction that would kill her (the killer). Just seeing the agony ofrealizing what she'd done was enough to send chills down your spine and make one misty-eyed.
Seeing Jodie break down in the car after Takagi confirms that the fingerprints on Conan's phone match those of the man found in the car, seemingly confirming Akai's death.
Then there's one of the saddest episodes ever; two partners owning a small TV shooting company, who are obviously in love, ask Kogoro to star in their show. Later the Asshole Victim Producer is found dead in his apartment. Suspicion immediately falls on the male partner, who tries to cover it up for a while but ultimately confesses the crime. Instead, it turns out that the female partner had been the one who killed the producer for passing her male partner through hell for not accepting illegal money transfers on their porposed show, and then had committed suicide while she spoke to him on the phone. Upon finding the scene, the guy had immediately covered it up and hidden her body in the car trunk, ready to even take the blame to keep her name clean. Conan's line through Kogoro's mouth makes the man break down in tears ... and the audience, too *sniff*
Conan/Kogoro:Won't she be feeling cold, where you hid her, with all this rain?
The Detective Koshien case's end in the anime has a really heartbreaking moment: when the Sympathetic Murderer, the Amateur Sleuth Natsuki Koshimizu, explains why she killed her fellow sleuth Junya Tokitsu... for causing the suicide of her best friend Kana Mizuguchi, a young maid wrongfully accused of killing her boss. Not only we see flashbacks of Kana crossing the Despair Event Horizon as she's believed to be a criminal when she actually was not (the boss was a mentally-ill socialitewho actually killed herself) and cannot clear her name, but then we have Natsuki break down crying as we "witness" the flashback with the last moments of poor Kana, right as she throws herself off a cliff and into the sea.
Yone: There's not a single person on Earth that deserves to die like that. I'm not saying that I forgive Reika-san for the crime she commited... (closes Reika's eyes) But when someone dies, it means that someone else's heart is stricken with grief. Even if I'm the only one in grief, that's more than enough...
The case introducing Tooru Amuro, with Kogoro's school friend Raita Banba. The night before his wedding, the bride, Hatsune Kamon, burns to death in her car. He's a suspect. Raita and Hatsune shared everything: Not only could they tell what the other was thinking even they were being silent, but they had the same birth date, same blood type, and they'd even been rescued from the same fire as infants and were both adopted. Yeah, I think you know where I'm going with this. It turns out that Hatsune was afflicted with Turner syndrome and that she and Raita are twins. She had suspected something was up and had used DNA sequencing to find out the truth. She'd received the call confirming it and killed herself in the first suicide since volume 1.
A minor one, but in the fifth movie, Sonoko styles her hair like Haibara, which surprises Conan and causes him to blush. Sadly, Ayumi watches from the car and is about to cry, that she doesn't have pretty hair. Poor girl.
Anything about Honjo Nanako from 13th movie. Her Heroic Sacrifice is very memorable.
The ending of "A Small Client".
In the final episode of the live-action series, there's the apparent death of Ran. Shinichi loses it trying to get to her body, while ignoring the police's efforts to find out what they can from him. And there's her father's response:
It's a lie, right? It's absolutely a lie that Ran is dead, right? She's only seventeen! What would my seventeen-year-old daughter die from?! *grabs Shinichi* Answer me, Boy Detective!