One early story comes to mind, A Mother's Love. It involves Usagi encountering the mother of a corrupt village ruler. We learn that the villain Used to Be a Sweet Kid. The mother tells Usagi to kill him, before claiming she was just joking. One night, Usagi finds the ruler dead with her mother cradling his body, revealing that she killed him herself. She begs Usagi to kill her, but he at first refuses. The issue ends with the mother singing a lullaby to her dead son before Usagi kills her off-panel and exits the house with tears in his eyes.
Noodles is a big one. Usagi encounters Kitsune, who has made a good friend in a huge, seemingly developmentally challenged man simply called "Noodles" (as he can tell her no other name), who helps her during her pickpocketing by hiding her in the soba box he carries around when she runs from the law. He is every bit as gentle as he is huge, with Kitsune describing him as a "child in a giant's body" and expressing interest in building a new life with him. However, a corrupt yoriki (high-ranking police official) decides to frame Noodles for the recent crime wave he has caused due to his debt to yakuza gamblers, and within merely a day, Noodles is captured and publicly executed by crucifixion and being stabbed in the chest with spears, with poor Kitsune begging for his release and screaming it was her (despite her little pickpocketing having nothing to do with said crime wave) before breaking down sobbing. Also a case of Beware the Nice Ones as Kitsune sets one hell of a revenge in motion, orchestrating events to have the yoriki not only outed for his corruption but ordered to commit seppuku.
Kitsune's whole life has been one long string of these, almost making her carefree attitude a case of Stepford Snarker. Aside from the death of Noodles, the worst blow was arguably the loss of her adoptive "sister" who taught her how to steal and survive on the street. One day she tried pickpocketing the wrong person, a samurai who had been present when they pulled an earlier scam, and Kitsune found her dead in the street.
The stunner at the conclusion of Fathers and Sons. Right at the moment when Usagi decides to not tell Jotaro of his true parentage, even though it breaks his heart... right at the very moment he's almost out of earshot, a tearful Jotaro confides that he knew Usagi was his father all along! If that doesn't make one a little misty-eyed, nothing will.
The ending of Senso, even if it is non-canon. Usagi manages to destroy the last Martian tripod, but the surviving martian pilot mortally wounds him in a Last Breath Bullet moment, leaving him dying in the arms of Jotaro and Tomoe. Jotaro and Usagi finally acknowledge each other as father and son, realizing that both of them had known all along. Usagi has enough time time left to pass his swords on to Jotaro, and tell Tomoe he loves her before dying from his wounds, leaving Jotaro and Tomoe sobbing over his body. It then cuts to the far future with Space Usagi telling a school of students about his ancestors deeds and the history of his ancestral swords.
One early story revolves around a woman making a traditional memorial figure for her dead child, who had been murdered by outlaws. According to Shinto belief, the souls of murdered children inhabit a bleak, restless afterlife, which the statues are supposed to alleviate by passing travelers offering token gifts. By pure chance, the outlaws attempt to ambush Usagi at the same road the statue has been placed, and he kills every last one of them. The final page has the mother noticing that the statue seems to have changed to a more relaxed facial expression, implying that the child's spirit is now at rest.
One story is a flashback to Katsuichi's youth, and reveals what happened to his lover, who had only been hinted at before. She was the daughter of the leader of a rival sword school, and the head student wanted her to marry him so he could inherit the school when the master died. When she refused, he killed her, and intended to kill Katsuichi and pin her death on him.
The conclusion to the "Red Scorpion" multiparter. The sensei of a sword school fallen on hard time kidnaps the son of the local magistrate while pretending to be the leader of the Red Scorpion gang in the hopes of extorting enough money to keep the school going. This fails completely as the real gang leader had been the magistrate himself the whole time and while the sensei and his students manage to defeat the real gang, he realizes his desperation drove him to complete dishonor, and ultimatly for nothing. He tells his students that he can only teach them one final thing, how a samurai dies, and asks Usagi to be his kaishakunin (second) for the seppuku ritual. Usagi accepts, and the final panel shows his remaining students weeping over his body.
The death of the tea master from #150, who commits seppuku to spare his lord from dishonor because the sadistic Spaniard Rodriguez had demanded to witness a seppuku as the reward he was promised for defeating the lord's men in a duel, and he wanted the person who dies to be significant so demanded the life of the near-universally beloved tea master. The Tea Master complies with his lord's request without complaint, much to Usagi's sorrow and rage. The story in question was inspired by the real-life seppuku of the famous tea master Sen no Rikyu, who was ordered by Toyotomi Hideyoshi to commit seppuku in 1591 due to political differences and Rikyu's excessive independence.
The Hero: Usagi meets a woman on the road, a poetess trapped in an unhappy arranged marriage to a minor lord with a higher status in court and a drinking problem. The husband can't stand that her fame outstrips his own (and due to the peace, has no way of advancing via his martial skills, hence the drinking). He eventually murders her, then realizes that even in death his wife will be more remembered than he, and commits seppuku (blaming his wife for it, of course).
