Tear Jerker / Basilisk

• In Basilisk, the end of the "fight" between Oboro and Gennosuke, specially when she stabs herself to die with honor after seeing she won't be able to kill him, for not only that she loved him but their duel was unfair and completely manipulated by external forces .
• Hotarubi's death was as sad as this one as well. I bawled when she, almost dead out of blood loss coming from having both of her arms cut off and being stabbed in the chest, weakly calls out to her dead husband Yashamaru with her last bits of strength, so her own murderer doesn't have the heart to say he's not Yashamaru so he just nods and lets her die in peace..
• And it may generally come in behind all these, but Koshirou's death in the manga really got to me, along with Akeginu's undignified and miserable end.
• Don't forget the scene in the last episode where Oboro imagines how her wedding would have gone through, if only things didn't go as... wrong as they did.
• Let's not forget the gruesome yet heartbreaking way Okoi died at the hands of Nenki and how her last moments with her brother were. Just when you thought she was about to get away, especially after avoiding rape twice! And then we have Saemon-as-Yashamaru as the recipient of her last words, unable to grieve and mourn for his beloved sister no matter how his heart is breaking right there.
  • As for Yashamaru, he died a man and his supposed "murderers" were comrades helping each other, and Gyobu didn't necessarily plan to kill him either.
• And if we go to something else than deaths, seeing in the anime how Kasumi Gyoubu became the ruthless Bare-Fisted Monk we know... Damn, it hurt. Poor child Gyoubu and his Disappeared Dad. Damn it.
• Jingoro's death is part this, part horrifying. Seeing him melting in the ocean while he desperately calls for help (which Akeginu was about to give to him) gives both chills and sadness.
• Nondeadly one, there's the scene where the recently blinded Koshiro believes that someone, maybe Gyobu, is approaching and reacts... only to find out that he almost hit Akeginu. His breakdown that follows is really sad to watch. Add it the one he has when Tenzen's trying to rape Oboro on the ship and he's torn between the loyalty to the man who raised him and the love for his lady of liege and you can really say that he qualifies as a Iron Woobie.
• The Cold-Blooded Torture that Kagerou was subjected to reaches this extreme when the same woman that she wanted to murder out of jealousy, Oboro, blindly stumbles into the place where Tenzen is torturing her, begging him to spare her. You know your life is simply terrible when the one who shows compassion for you in one of your darkest hours ever is someone whom you loathe and want dead.
• Really, the biggest tearjerker of the series is how all of this death and tragedy could have been avoided had the participants all just let go of their hatred towards one another. Both the Kouga and Iga clans are not too different from each other, and indeed, if united, could both prove to be a powerhouse of a clan in the whole of Japan. But members from both factions just hate each other so much that the very first opportunity they get to kill each other, they take immediately. It ends with everyone dead, and that just makes it so much worse.
  • Another big kick to the gut is that this could've ended ages ago with Danjou and Ogen's wedding. It's just that they put the village's desires before their own happiness in the manga. It was implied in the anime that an attack on Iga was engineered by Tenzen, so it was much more personal for the two. It's particularly sad because Danjou and Ogen both knew they could've kept the peace for their grandchildren, but feel obligated to let their clans, who still feel the need to avenge themselves of grievances that happened 400 friggin' years in the past, fight. After the two kill each other, it's shown that despite having started their own families, they never did stop loving each other.
• Saemon's interactions with Akeginu in episode 20 of the anime. While disguised as Tenzen he is kinder to Akeginu, his enemy, than the real Tenzen would be. He allows her to keep Gennosuke's Flute, and laments on the mystery of his enemies' heart, forming a connection between the two. Only for him to backstab her and allow her to be killed by Kagerou. She dies alone and confused, giving one last look to Saemon who is unable to look her in the eye. After this he has an Alas, Poor Villain moment and recalls Gennosuke's words about getting to know the Iga but laments that at this point, it's too late.