These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Noriko, known as the Blood Princess has had homicidal tendencies since childhood, where she would always beat her cousin Tomoe in spars to inflict as much pain as she could. In the present day, Noriko runs a mine, using slaves that have been press-ganged into service and worked to the point of death. Should any slave falter, Noriko promptly beheads the nearest one to serve as a morale-booster for the others. When she captures Tomoe, Noriko delights in treating her as a slave and when Tomoe refuses to perform the labor, Noriko furiously cuts down a random slave woman. When Tomoe immediately obeys to stop more death, Noriko sneers at her for caring about those of low birth. To conceal the mines, Noriko plans to blow it up, with every slave inside after all its resources are gone. She also reveals that she and Tomoe are actually ''sisters'' and when their father refused to acknowledge Noriko as his daughter, she murdered him, just as she had the man who raised her for for being weak. She reveals this while savagely beating Tomoe, taunting her that it's Tomoe's fault that he died.
General Fujii was the head of a gang that took over a village. They reduced the workers to slaves, and ordered them to farm and cultivate for long hours. They would continue to do this until the tax collector came, at which point they would just kill all the villagers and go to another town. When Usagi infiltrates them, he's discovered and tortured, with Fujii taking his swords. When the peasants revolt, the slaughter their way through them, and Fujii abandons most of his men to die or face the police. He and his loyal Dragon take over another gang and launch raids on a village, where he almost murders the elderly headsman for refusing them. When the heroes attack the gang to take him down, he abandons his dragon to run.
General Fujii is such a bastard that even the aforementioned gang becomes repulsed by him. Usagi actually repeatedly calls him a "monster".
Genius Bonus: The woman who's a secret Christian wears a kimono with a subtle cross design, which was how real secret converts ID'd each other.
Hilarious in Hindsight: In one issue Usagi is forced to wash dishes at an inn he can't pay for his meal at due to being pick pocketed. When some ruffians break into the inn after he's finished they even call him the Dishwasher. Usagi was the first Dishwasher Samurai.
Parts of the first story arc in Space Usagi (1992-1994) are similar to The Phantom Menace (1999; references to the original Star Wars trilogy are pretty much mandatory): both feature a princess trading places with her bodyguard for safety (in Phantom Menace the (future) hero falls for the bodyguard/handmaiden who'd really the princess while in Space Usagi the "princess" is actually the bodyguard) and the hero dueling the Big Bad's Dragon which ends with the bad guy getting sliced in half and falling from a high place. The second story arc has our hero discovering that a man he thought of as closely as a relative has become corrupt.
I Am Not Shazam: "Yojimbo" (bodyguard) is not part of his name but sometimes his occupation while on the warrior's path. The 80s cartoon took "Usagi Yojimbo" for his name, the 2003 one correctly had "Miyamoto Usagi".
Nightmare Fuel: Jei's introductory issue. The atmosphere was very haunting. What really set it was seeing Jei go from kind-enough to give Usagi a place to stay in the rain to a ravaging madman in the blink of an eye. When Usagi first fought him, he was close to death, had the bolt of lightning not interfered. While Jei was originally meant to be a one-shot villain, the ending left the reader wondering if he were really dead.
Tear Jerker: Almost every story. Aren't you reading these?!
However, violence is never trivialized. Usagi (and other morally upright types like Sanshobo and Katsuichi) does not kill wantonly, rarely strikes first, allows flight and accepts surrender; only the villains regard violence as a quick and convenient solution. It's kid-friendly to the extent that the author presents avoiding combat as a morally superior choice.