In episode 2, during the dog race, Ganta gives up the ball that would allow him to win the race to save Shiro from falling. Winning the race would have allowed Ganta to purchase the antidote to the poison that is regularly injected into his body. He had every reason to believe this course of action would kill him.
Minatsuki's penalty game. Seeing her trying to be brave was moe enough but then Nagi pulled strings to fixed her penalty to a hair cut. The happiness on her face, mixed with the relief on Ganta's, is wonderful.
After Ganta's Nakama turn against him, they treat him in a really awful way and even vandalize his room. After this, it's then shown that they aren't the only ones that hate him- the whole prison does. As he's attacked by some other inmates, it looks like he's nearing a Heroic BSOD- making the panels where Shiro rescues him and then innocently asks if he's okay a really powerful You Are Not Alone moment. Ganta's face in panel 2 is so adorable that the moment becomes a Tear Jerker, in a really sweet and non-depressing way.
And is then subverted by the What the Hell, Hero? that follows. Which is then subverted again by it being a lie to protect her- heartwarming again, because up until then, Shiro had been the one protecting him.
"If you guys hate Ganta, that's okay... I'll just make up for it by liking him more."
Makina announces that she'll be leaving her position as head guard of Deadman Wonderland, and will instead devote herself to leading a "Special Forces" group dedicated to bringing justice to Tamaki and the rest of the prison. The heartwarming part comes in when she announces that she has made sure that none of her men will be at fault for her actions, and she even goes as far as to prepare a retirement fund for everybody, and sends letters of recommendation to other relevant facilities. And what do her men do in response? Quietly pack their things and head out, or hand her over? Nope! They all resign and proceed to join her Special Forces group as well.
And their efforts ultimately pay off. They reveal to the world the atrocities going on in Deadman Wonderland, free every innocent prisoner and make it clear to the world that that many of the Deadmen were framed so that they could be dragged to Deadman Wonderland against their will. Ganta and every one of his innocent friends are completely absolved of their crimes.
Young Ganta (to young Shiro): "From now on, you are my treasure!"
And, as noted further down, a second, arguably even more CMOH instance happens when Ganta does it again to Shiro at the end of their final battle, stating she's his forever and that he'll love her no matter what she's done.
A rather surprising one in the latter chapters. Shortly after the mission to return to Deadman Wonderland begins, Yosuga decides she's going with them for the sole purpose of protecting Mockingbird, someone she cares deeply about as her 'younger brother,' and even admits to Ganta that she might be in love with him. After being rejected and effortlessly (and judging by the lack of apparent injury, rather painlessly) tossed aside by Mockingbird when she finally confronts him, she steals medical supplies from Makina, finds him after he just got beaten by Senji. She saves his life, and then treats his wounds. When Mockingbird asks why... this is her response.
The fact that she is clearly aware that Mockingbird is now Hagire Rinichirou makes this a borderline tearjerker as well. She seems to think her Toto is still in there, somewhere, and refuses to believe otherwise.
There's a rather twisted one that oddly works well in Chapter 55. Having fully told the truth of her life, Shiro admits that her wish is for Ganta, the only person Shiro loved and fully trusted, to kill her. Without a moment of hesitation, he accepts her wish. She smiles and responds, "Thank you, let's play like we did when we were kids..."Man, where's the kleenex box when you need it?
And then a purer one in chapter 56.2, when it's revealed that Shiro really doesn't want to die, but just live a normal, happy life together with Ganta. He proceeds to draw his symbol on her hand, similar to how he did so when they were kids ("You're my treasure!", remember?), and states that regardless of how unforgivable her crimes are or how irrational their love is, he loves her, she loves him, and she shouldn't feel bad for doing so. They happily embrace, even as they may or may not have died in the following moments. Now THAT'S one hell of CMOH.
The ending. Every who deserves a happy ending gets one. Everyone. Yoh gets to live with his little sister Minazuki again, and they're going to school. Senji isn't hindered by the injuries he received when fighting as a Deadman. Masu even becomes a successful professional eater. Makina eventually gets over her paralysis and goes back to being a leader in the military. Karako becomes a nurse. Ganta gets to go back to school and live normally, and when it looks like Shiro is stuck in a coma with Ganta futilely visiting her, the manga ends with her opening her eyes and smiling.
Also, Hitara teaches college philosophy and Chaplin becomes an actress and play director.