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Tear Jerker: Samurai Deeper Kyo
Saisei's death. Especially since it's also probably the first time we see Akira show real emotion or regret.
Hishigi dying as we learn just how far he's gone to try to save the Mibu clan and his friend, and his speech to Fubuki just before dying in his arms. Also, the memories he gives to Akari directly before sacrificing himself.
Kyo ordering the others to run as he has been horribly wounded and the Crimson Tower is collapsing around him.