Tenma pleading to a BSOD-ing Nina to not kill herself.
Additionally, Eva's Doomed Appointment with Martin. That one second of pure joy she experiences when she thinks that he actually did come only serves to make the scene that much more painful when she realizes the truth. Naoki Urasawa apparently feeds off of crushed hopes and dreams.
Even worse than that, though — did she believe the twin she left behind would be kept safe, or the one she took?
Once upon a time, there was a detective (Richard Braun). We saw him for just, like, three episodes, but we grew fond of him, after all. He had a lovely daughter that he was finally going to meet. He didn't drink anymore, he was getting his life together, and he had finally found peace. Then Johan happens, and something inside us dies; poor Richard just had to fall into his trap, just the night before he was supposed to see his daughter (which, unfortunately, did not happen). *Sigh* if only Richard had simply NOT answered the door when Johan came knocking; or, at the very least, just simply and politely refuse (and say he's busy or something) to go out with him! Of course, that is not to say that it is Richard's own fault that he got murdered — afterall, Johan is a master-manipulator. And if Dr. Reichwein and/or Gillen had been able to contact Richard to warn him about Johan, would it have made a difference? Who knows... In the manga, they even name the 7th book after the guy and make him the main character in it... adding to the attachment and subsequent sadness. This MAY have been more bearable if Johan had been gruesomely killed at the end of the series, but...
"It's okay, you can have a drink now." Get's me every time.
"Say my name." "We don't have names."
Nina... you bastard... why didn't ya just... forgive... him?
Karl emotionally reading to Schuwald on the phone for what he thinks is the final time, which is quickly seamlessly married to a Crowning Moment of Heartwarming as Schuwald arrives and reveals that he knows Karl is his son.
Karl, Lotte, and Johan take Schuwald to his "special place"; a beatiful forested lake. Karl and Lotte try to disguise the fact that it's now a construction site, but Schuwald, despite being blind, still knows, as he can no longer hear the calling of the wrens. Johan, however, describes the spot so vividly that Schuwald is able to recall it in his mind. With tears streaming down his face, he says simply, "I can see it well."
Probably very subjective, but this troper shed a few tears for Roberto when it's revealed shortly before his death that he was the boy Grimmer befriended in 511 Kinderheim. Made even worse when one realizes that since the children there decided to remember details about each other rather than themselves, it was very likely that Roberto knew Grimmer's real name.
Speaking of Grimmer: "Doctor Tenma... What does my face look like right now?"
The entire Ruhenheim arc for this troper, because she knew what was coming. Ditto the elderly couple shown previously who show brief kindness and warmth to two lost, wandering children, and are killed for it.
This troper actually got a little misty-eyed (out of joy) in the last episode, when Nina finds out she aced her thesis. After all that she had to endure, it was such a relief to see that her life was back on track, and that regardless of everything she'd lost, she would have a future.
Nina and Dr. Gillen visit Franz Bonaparta's cottage in Ruhenheim, whereupon it is revealed that Johan had already visited the cottage and perused through the various sketches of himself and Nina. Nina, somehow in tune with her twin brother's emotions in light of their folie a deux-like tendencies, states that he cried over the portraits, possibly indicating the first exemplary moment of real sincere sadness sans ambiguous crocodile tears that Johan has exhibited. If the implications of this aren't tearjerking enough, then this fancomic depicting the unseen moment should serve to rend your heart: http://sinemoras09.livejournal.com/467347.html.
The story about Bernard, the soldier who taught Tenma how to shoot. He'd adopted a girl whose mother he'd shot, and told Tenma that she'd never smiled since that day and that she'd hate him for the rest of his life. Thanks to Tenma, she seems to recover. The last shot we see of them is the two holding hands, walking home in the rain. The girls looks up to him and smiles.
From episode 13: "I finally have your undivided attention".
Wim. Just...Wim. His mom abandoned him, his alcoholic dad beats him and makes him work for booze money, and he gets tormented constantly by the other kids for it. The old man he works for, revealed to be Franz Bonaparta, is the only person shown to be consistently nice to him. Then Johan and Roberto come to town and kickstart a massacre of everybody there, and dozens of his neighbors are murdered, his employer among them. Then when Johan realizes that Tenma will not shoot him on sight, he decides to move things along by putting a gun to Wim's head and telling Tenma that if he doesn't kill Johan, Johan will shoot Wim. And then Wim's father shows up, and upon seeing Johan with a gun pointed at his son, he freaks out and puts a bullet inJohan's head, and ends up getting arrested for it when the authorities finally show up to help. The last we see of Wim is him being pulled away from his father by policemen, crying and desperately trying to tell them that his dad was in the right. Keep in mind that he's no older than Dieter.
Wim: Dad was trying to save me! ...My dad's not a murderer!
Everything about Runge's near-nonexistent relationship with his family, especially this line concerning his daughter:
Runge: We lived our lives without knowing one another.