In the revision, one flashback involves Souichi breaking down slightly as he's reminded of his and his brother's fates, with him begging Souji not to die before him.
Later on, the reader gets to see, briefly, the "slaughter game" from Souji's perspective. One panel that stands out in particular is, again seen from Souji's eyes, is his fallen, half-dead brother. It's made even worse when you recall that Souji is only 12 years old and that Souichi is normally a near-infallible Badass.
During the above moment, when Souji brutally murders two hunters in order to save Souichi and Takeru. The fact that Souichi, of all people, looks utterly crushed really makes the scene hurt. Soon after, he ends up breaking down, revealing how angry he is at himself, before relenting and agreeing that he needs Souji's help. The revision of the scene makes it even worse.
The revelation of how serious Ken's condition is, between Fujimaru's worried expression—a face that he definitely hadn't made up until then—and Ken collapsing in his arms.
Ken's attempted Heroic Sacrifice. He isn't even on the heroes' side yet, meaning that none of them were expecting it—least of all Fujimaru, who's the most devastated by it. The look on Fujimaru's face when Ken smiles at him is especially heartbreaking, as it sinks in that Ken—likely the only real connection Fujimaru's had for most of his life—is doing all this to save him.
In the revision, after Souichi and Souji come to an understanding, Takeru is watching in the background with a smile. There's a moment, however, where his expression falters as he's reminded of how his own brother would comfort him—his brother who, last he saw him, tried to kill him.
Seeing Shirayuki look so miserable after being taken back to the government, with her crying in her dreams, is rather painful.
Briefly, after Takeru shoots down a helicopter, a tattered family photo of one of the soldiers he just killed flutters by Takeru's face, just to reinforce the aversion of What Measure Is a Mook?.
The Shibuya arc is easily one of the most depressing arcs of the series, making it full of these:
A minor example, but as mentioned above, seeing Souichi's composure falter—in this case, seeing him scream so badly in pain thanks to the operation he's going through—is a bit painful to see.
Ken's thoughts as he blacks out, after Haruyama nearly kills him. His first is to Haruyama, wondering why the other man would be making such a face over something that he personally did. His second is to Fujimaru, apologizing as he knows that Fujimaru must be calling out for him right now but he can't respond.
Uzuki's death, especially with Takeru's decision to Let Them Die Happy. Not helping is the accompanying illustration to this chapter: a picture of the character in question, smiling happily.
This is the arc where Takeru begins to falter in his optimism, with the entire arc being the gradual process of his breakdown, even if he recovers afterwards. You'll want to give the guy a hug at some point, whether when he wonders if a happy ending is possible after all or when he gets increasingly desperate in his fight against Tama or when—for the first time in the series—he finally breaks down crying.
Takeru: 'After we defeat the old hag... is there a way for everyone to honestly be happy...?'
Haruyama and Mogami end up dying almost immediately after their Heel–Face Turn, with their deaths in conjunction with the revelation that Souji's gone blind and Souichi's de-aged by another year. The depiction of the heroes—especially Takeru—staring at the wreckage captures perfectly the grimness of the entire situation.
The realization of how much Izumi's suffered over the last two years (especially on the day of the apocalypse) and what he's done in order to protect Takeru, especially as his past is revealed. The man doesn't angst about it much, which makes it all the more poignant.
When (it's implied that) Shirayuki tries to pull a Heroic Suicide by Izumi's hands, after which Izumi's horrified and tells her not to choose that path as Shirayuki cries. The idea, though, that Shirayuki was that desperate is rather sobering.
The panel of Tama sobbing into the late Haruyama/Mogami's jacket. Not helped by, like the above death, the accompanying chapter illustration depicting a happy scene of them together.
The story of Akane's past—specifically, how he became a doctor in order to save his mother, but she died before he could do so, combined with his sad smile and explanation that this is why he now wants to help the tekigousha.
The revision reveals exactly how Amagiya and Shirayuki met: amidst the corpses that was Amagiya's experimentation group, Shirayuki's going from corpse to corpse, desperate to find at least one person she can save. She ultimately finds that person in Amagiya, who chooses to live on for her sake.
Just before the final arc, there's a colour illustration◊ of the gang, eating flavoured ice. What makes it a Tearjerker is how happy and peaceful everyone is in a way that they aren't actually in-universe, with the text—"a scene of 'happiness' "—even rubbing it in your face.
From the finale:
Fujimaru sitting alone in the area where he's erasing all of the government data, tangled up in his own nerves and slowly destroying his own body with his ability. Outside, Ken is fighting with Ryuuichi and, for all Fujimaru knows, dying. It's a quiet, poignant scene where, in that moment, Fujimaru reflects on his life, thinking of his mother and what he did as Ward Chief in his hopelessness. That said, it overlaps with Crowning Moment of Awesome, showing just how far Fujimaru's come since then.
When Souji tries to comfort Ryuuichi by assuring him that Uzuki was happy and fulfilled in her last moments. The main Tearjerker, however, comes from seeing Ryuuichi lie on the floor, miserable and broken.
Takeru and Shirayuki's reunion. Shirayuki's a sobbing wreck, and it's really hard to blame the poor girl.
As Amagiya tries to kill Kuroyuki, having gone completely insane, he looks back at Shirayuki, who's crying over it all. The look shared between them sums up their entire relationship: that, above all, Amagiya would place his life on the line to protect Shirayuki.
Along those lines, Amagiya's 'death' that occurs immediately afterwards, both in terms of the scene itself and Izumi, when about to pull a Heroic Sacrifice, directing his thoughts towards Amagiya and how they can resume their earlier fight in the afterlife.
In response to Takeru's earlier worries over the impossibility of finding happiness, Akane states what is, ultimately, the true message of the story and what it means to keep smiling: not to hold out for your happy ending, but to make your life happy in the present.
The last moment where Takeru's optimism is needed: as he's gouging out the original from Shirayuki, he promises her that after all this, together with everyone, they'll go and make a grave for Amagiya. Shirayuki's Tearful Smile says it all.