Verdeman discovering his father advised a boy from Bonaparta's reading seminars to escape the program; a boy who has now become a happily married and perfectly sane man.
Nina, Dieter, and Lipski dealing with their collective horrible memories by spending a fun, tourist-y day in Prague making good memories for themselves.
Runge going out of his way to compliment Wim's new bike.
Karl taking Schubert, a man with terrible vision, out to a construction site that used to be his favorite spot, lush with greenery and with a giant lake. Karl almost tells him that it has been destroyed during construction, but Johan hands Schubert a single apple, telling him that it has fallen off a nearby tree. Schubert cries upon eating the apple, telling his companions that he can see his beloved lake perfectly clearly.
Especially poignant when one considers that this is Johan we're talking about, even if he is doing it with ultimate insidious and destructive intent...
Lunge: Dr. Tenma... I'm sorry.
Johan convinces a blind, bitter, aged billionaire that the desolate construction site that used to be his cherished childhood spot is still a beautiful lake by lying to him and handing him a sand covered apple. He even convinces him the birds are still there. It moved the old man to tears and it makes you wonder what sort of awful plans Johan has waiting for him. Assassination and arson, in case you were wondering.
The guy with the five spoonfuls of sugar belongs here, too.
Several of Tenma's previous patients blocking the hallway and allowing him time to get away. Later we see that they're all still working hard trying to prove his innocence.
After several occasions of Tenma leaving the restaurant leaving his food uneaten, the somewhat-grumpy waitress makes him eat a bowl of soup on the house.
Nina, Dieter, and Lipsky spend a day making fun memories for themselves throughout Prague, then Lipsky shows them his new puppet show based on Nina, that he wants to have a happy ending.
Verdeman lost all faith in humanity when he discovered his beloved father was a Communist spy. Then he discovered that his father advised one of the boys from the Red Rose Mansion reading seminars to escape from them. The boy took his advice, and in stark contrast to the rest of the children who went to the seminars, he has become a happy, well-adjusted adult.
Nina comes very close to shooting herself in the head, but Tenma reaches her in time. He carefully pulls the gun away from her, holds her tightly in his arms, and delivers a touchingspeech about how much she means to him.
The couple introduced in the Ruhenheim episodes, Henning and Franka, holding each other near the end of the series. Considering how they always bickered, even when first introduced, and Franka's obsession with winning the lottery and blaming her husband for not having enough money, after the Ruhenheim massacre is finally stopped and the police come their reconciliation is heartwarming. Seeing her husband go off in a hurry to find and get back her winning lottery ticket, Franka desperately calls after him: "Honey, it's okay! We don't need it. I am content to live this way, it's enough for me." Then they finally smile at each other through tears and embrace. Even the policeman that was asking them for I Ds just smiles and walks off, saying they can show them to him later.
Even after everything that Johan has done to her, Nina genuinely forgiving Johan can be considered a heartwarming moment. The entire series, she's been hunting him down and set to kill him, but Nina actually finding it in her heart to forgive Johan is heartwarming in itself.
In her interview in Another Monster, it's shown that Eva still continues to order coffee over alcohol after three years. D'aww.
As Tenma passes Lunge in the police station after being arrested, Lunge hint to him that the best thing he can do during interrogation is to show no emotions and say nothing. After doggedly pursuing Tenma throughout the whole series, it is the first time he shows that he believes that Tenma is not guilty.
The time where Nina/Anna visits her old friend and father-figure Mr. Rosso, owner of an Italian restaurant and ex-hitman, was very heartwarming and a nice breather from all the tension and suspense of the story.
Throughout the series, Nina has had momentary flashbacks of an unknown, menacing-looking man (implied to be one of the people who experimented on her and her brother) reaching for her and saying, "People can become anything." Towards the end of the series, it's revealed that this was Franz Bonaparta, having a change of heart and letting Young!Nina go free. He was reaching out to give her a comforting caress to the face.