In his battle with Ichi and Hajime, Hitara appears to finally get some closure with his past. Makes sense in a manga like this that a Tear Jerker would occur as two psychopathic thirty-year old "children" burn alive.
The ending theme for the anime, showing the cast's happier times. Especially the slides of Little Genkaku happily meditating under a waterfall, Nagi with his wife, and Seiji with his crew.
When the twins tell Hagire, shortly after throwing themselves onto Senji's blades in order to protect him, that they love him. Hagire replies, "I never loved you." And they simply smiled, and said, "We know that, of course."
Shiro's backstory. All of it. Who knew that behind the sweet, bubbly facade lies a broken, scared girl who only wants to purge the monster inside her and experience freedom for the first time in her life?
From the anime, Shiro breaking down in tears whilst eating cookies she was going to share with Ganta — until he punched her in the face and told her to get lost after she destroyed a data chip (spoiler: actually a bomb) that was a way of bringing Deadman Wonderland down in order to save his life.
Shiro: I turned into Aceman to help him, so... why does Ganta hate me so much? How come the cookies don't taste good? I'm eating and eating, so how come I feel all empty? Why do I even care...?
Seeing Warden Makina wheelchair-bound is really upsetting, considering what a badass she was.
Nagi's back story, and his sobbing meltdown in episode eleven.
Then episode 12 has Nagi's death, where he quietly muses to Karako about the rain... not realizing that it's her tears.
Toto's last moments as himself. Right before he loses his body, he shouts "I won't die, I won't! There's someone—"
Toto's actual final moments. It gets so much worse when you consider Hagire killed Yosuga using Toto's body just minutes earlier, when all she wanted was to be with her Toto again, granting her wish for them to die with each other in the worst possible way.
Chapter 55. Just when you thought Shiro's backstory couldn't possibly get any more tragic...
An entry from a fan-run Tumblr blog for Shiro makes her wish incredibly worse. One fan is upset that her wish is to die and asked her why she feels that her wish is the only solution. This is her response.
The above, of course, sets up the Final Battlebetween two childhood friends and lovers. If that wasn't bad enough, remember that Shiro is a Death Seeker and that Ganta's powers will ultimately kill him. The likelihood of either one, or both, of the characters coming out of this one alive looks... slim at best.
The Dark Reprise of the 'Woodpecker Song' being recited on the pages where the fight happens makes it so much worse. Yes, they somehow managed to make that song even sadder in context.
Chapter 56b. Shiro resents not being able to live a proper life and feels incredibly guilty by all the havoc and destruction she causes. But, she doesn't want to go through her wish and states she wants to live after all with Ganta...
Which is followed by a happy, if still tearjerking, moment when Ganta writes his first name initial in Shiro's right hand and offers to be with her for the rest of her life. She accepts.
And then their Branches of Sin react, triggering an explosion that engulfs the two. Talk about one hell of a sobering Cliffhanger.
There's a flashback where Shiro is trying to share her pudding with a Aceman action figure that was so simple and so desolately lonely, especially when she admits to herself that Aceman can't eat with her and Shiro's tears come.