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Tear Jerker: Sakamichino Apollon
Sen telling Kaoru about his childhood causes Kaoru to start crying, half because he felt like an ass for thinking his life was so bad, half because it was just plain sad.
The episode when Kaoru meets his mother for the first time. Especially at the end, when she starts crying as he's leaving and mouths "I'm sorry". He shakes his head, to show that he is not angry at her for what happened.
The Gray Rain of Depression that occurs when Kaoru learns his father will not be able to stay for long when he returns home.
The flashbacks shown when Kaoru remembers being rejected by friends in the past.