The scene where Aya's mother placed a charm on her is pretty touching, too. It's especially touching in the Good Ending.
Aya's innocent love and devotion towards her father, even though she knows what he's doing is wrong, is either this or a Tear Jerker.
Maria being taken in by the doctor. She was originally homeless and starving until the doctor took her in. True, she was going to be a test subject, but he decided to use her services.
In a weird, twisted, Tear Jerker-ish way, the doctor himself is this. It's mentioned in one entry of his diary that he "found a dead cat in [Aya's] drawer. Hiding it in a dresser... Exactly as [he] used to." When put in this context, he was afraid that Aya would turn out like him when he was young. His resolve is to turn his precious daughter into a doll so she isn't "dirtied" and doesn't make the same mistakes as he did. He really did mean it when he said, "I love you."
Aya sleeptalk scene in the If-Ending. As the blonde boy and Maria put her back in her room to let her rest after the doctor has died, Aya begins calling for Maria in her sleep, saying that she wants to live together with her. It's heartwarming that Aya managed to understand Maria's love for her father and will stay at her side, now that the doctor has died and they have no place to go. Especially considering how mistrusting and cold Aya was to her at the beginning.
Dio kissing Aya on the forehead to give her a good luck charm, just like her mother did.