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..
On the same note, this troper found Yashamaru's death quite saddening as well, especially after he dies after spending several episodes promising to himself that he would get back safely to his wife, the abovementioned Hotarubi. Needless to say, this troper found his killers' deaths quite satisfying, especially when one of the two murderers was stabbed to death by mere non-ninja mooks.
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.
I wonder how I could 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.
Actually, every single damn death in the whole anime was sad in a sort of way. If not because of the actual character, then for the clan. Inside the clan, all of them were likable characters and kind of a family. And just with the death of one family member, it will never be like before. For this troper, Akeginu's death was the saddest moment. She was so close to avenging Jingorou and Koshirou, but is stopped by Saemon/Tenzen, whom she believed to be at her side, gets stabbed with a blade, told that she would go to hell and Oboro would soon follow, then she is thrown down a bridge. What a disturbing and sad end. Thinking of the events of Basilisk as a whole, I can only think "What a Senseless Waste of Human Life". Damn shogun.
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 Famous 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 desperatly 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 following breakdown 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 simplyterrible when the one who shows compassion for you in one of your darkest hours ever is someone whom you loathe and want dead.