Eren, Mikasa, and Armin's friendship is pretty heartwarming. Eren was willing to dive into a Titan's mouth to rescue Armin. Mikasa is extremely protective of Eren and is willing to do anything, and go anywhere to be with him. When Armin tells her that Eren died for him, Mikasa, despite her devotion to Eren, never held it against Armin and still thinks of him as a friend. While not as obvious as Mikasa, Eren is protective of her as well. He is always quick to defend her and was horrified when he realizes that he unconsciously attacked her as a Titan. Don't forget the fact that despite Eren and Mikasa always having to save Armin when they were kids, they never once thought of him as anything but an equal. Or the fact Mikasa and Armin treat Eren just like they always have, despite him being able to change into a Titan. Everyone else is or once was horrified by this.
In the flashback where Eren rescues Mikasa from human traffickers, Mikasa, still in shock from the whole ordeal, mentions that she's cold. Eren immediately takes off his scarf and wraps it around her in a comforting gesture. The same scarf that Mikasa continues to wear as an adult.
The fact that after the deaths of Mikasa's parents, the Yeagers took Mikasa in without a moment's hesitation. And judging from what we saw of her interactions with Carla and Grisha, it's clear that they treated her with the same love and care they gave their own son. Though it came on the heels of one of the darkest times in her life, it is rather nice to know that Mikasa spent the aftermath of that horror in the care of genuinely good people.
When Armin gives Mikasa his remaining gas and plans to commit suicide to avoid being Eaten Alive, she tosses his remaining knife over the edge, and tells him to shut up and come with her because she wasn't going to leave him behind.
Right before Armin and Connie find Mikasa, she's about to give up and let the Titan eat her but wonders why she's suddenly fighting back. Her inner dialogue at first is utterly heartbreaking until she starts remembering that, as a child, Eren told her that if she doesn't fight, she can't win. This segues into her remembering how it felt to not give up, with Eren's "FIGHT!" in the background. Her inner dialogue all the way through goes something like the below, all with this playing in the background. Tears of happiness were shed.Better yet, see that scene here.
Mikasa: Why? I thought I'd given up. Why am I standing? Why am I struggling? Why? My life has no meaning anymore. What's keeping me going?(Eren: Fight! Fight! FIGHT!) Eren. (Eren: Fight! You must fight! Fight! FIGHT!) I'm sorry, Eren. I won't give up. I'll never give up again. If I died, I wouldn't be able to remember you. So I'll win, no matter what! I'll survive no matter what!
The stern-faced Mikasacrying when she finds Eren alive and well. The fact that he was found controlling the body of a Titan, and began killing other Titans after said Titan's body disintegrated, doesn't subtract anything from this. Additionally, when Armin sees Eren's regenerated arm and leg. They were trying to reach for each other when the Titan snapped its jaws shut and swallowed him; when Armin crouches down and laces their fingers together, he's making up for not being able to do it before.
Neither Armin and especially not Mikasa doubt a second before being shown to be willing to sacrifice their lives, social standing, and everything to run off with Eren after the military and pretty much everyone turns against him. It isn't even a plot point, it isn't discussed. Their support to Eren is a given and completely unconditional. That, my friends, is a true bond.
Mikasa needs a little more illumination here. She didn't abandon humanity to protect Eren. She had never cared about humanity in the first place. Her thought process seems to have gone like this: Eren = Titan, Titan = human's enemy, humans = Eren's enemy, humans = kill.
During Eren's trial, one merchant makes the mistake of assuming that Mikasa is a Titan too, because he's operating on panicked mob psychology or something. Eren takes offense to this, yelling that though he may be a monster, his sister has nothing to do with it.
The little girl thanking Mikasa for saving her during the evacuation of Trost. Made even sweeter by Mikasa's reaction; she smiles and salutes, making the girl gasp with admiration. It's a small reminder that despite Mikasa's enormous devotion to Eren, she does care about protecting the rest of humanity, at least a little.
In Chapter 17, Eren tries to impress Annie with his kick to which she teases back that he's hopeless at it. When he asks her about her technique, it's the only time in the entire manga to date that we see her sincerely smile. Also heartwarming because it signifies the beginning of an unlikely friendship.
Eren and Annie's relationship in general could count for some subtle heartwarming qualities. In the manga, it's hinted that they grew relatively close upon frequently sparring together, which culminates in Eren fiercely denying Annie being a bad guy and being accused of having "special feelings" for her, while Annie on the other hand admires Eren and only speaks fondly of him if he is brought up. Furthermore, Eren appears willing to give her more consideration over her crimes than he later does towards Reiner and Bertolt, where he falls completely into Black & White morality and instantly hates them with a passion. And while the anime basically cut out their relationship completely, it still added titan!Eren halting at the sight of her crying towards the end of their second fight, as if he was brought back to his senses when seeing Annie herself, and/or he couldn't bring himself to harm her personally.
When Eren first appears in his Titan form, the fighting pose he enters is the one Annie taught him (which is curios, considering Eren isn't even conscious at that point), serving to show the deep impression her tutoring had on him.
When Armin lies to Reiner and Bertolt about Annie being tortured, we see not only their reactions, but Eren's as well, briefly looking horrified as if the thought of Annie being tortured doesn't sit well with him. While one could argue he was reacting in shock to the lie, his expression still looks more worried than shocked.
Marco assuring Jean that he would make a good leader several times during the Battle of Trost; their interactions in general are rather sweet, especially in the anime. Doubles as Tear Jerker when it's revealed that Marco died in the Battle of Trost, causing Jean to freak out.
Levi's introduction initially makes him seem like a cold neat-freak who gets pissed when he gets blood on his hands, but when his subordinate is bleeding to death, he ignores the blood on the injured soldier's hands in order to hold them and reassure him that his sacrifice was not in vain, and that he'll exterminate all of the Titans.
It's a small one, but in Chapter 20, Hange talks to Eren about her experiments with Sawney and Bean, as the rest of Levi's squad leaves the room, knowing what's going to happen. From her words, you get the impression that Hange is aware of how she comes across. Eren asks to hear more about her experiments, anyway.
Eren unknowingly transforms into a Titan and Levi's Special Operations Squad assigned to protect and watch him immediately turns on him. After Levi explains their reasoning to Eren and they find out that he really did transform unknowingly, Eld and Gunther admit that they acted too rash. The squad members nod at each other knowingly and simultaneously bite their hands like Eren does when he transforms into Titan (even Oluo), and tell Eren that it's impressive how he can do that despite the pain. Then, a clearly guilty Petra apologizes to him for being rash and asks Eren to have faith in them from now on, as they will try to have faith in him as well.
After their failed mission against the Female Titan, Levi takes the badge off of one of the deceased. We cannot confirm who it is, but it is believed by some to be Petra Ral's badge After another soldier risks himself and others attempting to recover the body of his dead friend, Levi gives him the badge, telling him that it belonged to the man's friend. Doubles as a Tear Jerker.
Sasha rushes to a village to evacuate people. She finds only a woman being eaten by a Titan while her child sits there with a blank look on his face. When it becomes clear that she can't kill it, she grabs the child and runs. Along the way, she tells the child to keep running and not stop until she finds people. After successfully blinding and escaping from the Titan, she rushes on to find the child only to discover that she's already been picked up by villagers, Sasha's father among them. Her father tells her what the girl told them and comments that Sasha has become a splendid person.
Hannes' talk with Mikasa and Armin, sharing army rations and reminding them how they would always help Eren whenever he picked fights. This motivates them to get into shape to rescue Eren from Bertolt and Reiner in the face of certain failure.
In Chapter 48, Ymir becoming terrified that Krista will hate her for the choices she's made to keep herself safe, and Krista assuring Ymir that, no matter what she does or whose side she ends up on, Krista will always stick by her.
In Chapter 50, Mikasa smiles and thanks Eren for everything including the scarf that he'd gave to her while being surrounded by Titans with all hope lost when everyone in the unit is completely surrounded.
Eren replying that he'll always wrap that scarf for her. As Eren reveals his new power and saves the day.
The moment in itself might double as Fridge Brillianceconsidering how they're surrounded by soldiers being eaten and fallen comrades in general facing certain death. Mikasa delivering her speech in the middle of it all is probably meant to symbolize her catch phrase of "The world is a cruel place, but it's also beautiful."
Doubling as a Crowning Moment Of Awesome, Krista boldly correcting Connie about her name and then tearing Ymir a new one for lying to her once again. Followed up immediately by declaring that from now on, they should live for themselves only and that she will never fear anything as long as they can be together.
There's also Ymir, in Titan form, petting Krista as a means of saying goodbye to her so she can to go with Reiner and Bertolt.
In Chapter 52, although it's a minor one, when some Military Police members start physically harassing Hange after she starts questioning them about Pastor Nick's death, Moblitgrabs one of them by the wrists with a glare that could melt the sun and very firmly states their positions in a way that demands respect from them.
Relatively minor, but Hange comforting an obviously rattled Levi after it's revealed Titans may actually be humans in Chapter 51 with a firm, "Didn't I say that it wasn't confirmed yet?" that goes against everything she had said up to that point. Then, Levi returning the favor in the next chapter when she is noticeably upset about Pastor Nick's death and her part in it, and as a result is too afraid to try anything else, although it's more of a What the Hell, Hero? speech. Point is, it's obviously tailored to her needs at the moment, and at the end he gives her the choice of what they should do next (not to mention he calls her by her name and nothing else throughout the entirety of it, a rarity up to this point in the story).
In the beginning of Chapter 51, Connie has collapsed in tears following the horrific mission, and Jean takes a moment to get him back up. It's quick but helps to reinforce how much Jean cares for his teammates.
In Chapter 54, Eren admits that he always found "Krista" to be a bit creepy and unnatural, but he thinks that Historia is a sincere and normal person.
Jean handling the Dirty Old Man for Armin, who previously molested him in the last chapter. Later on, we see Jean consoling him after the whole ordeal.
In Chapter 56, Reebs spoiled apprentice/son Frager, who told humanity's strongest to get him a drink in the most obnoxious way possible, said that he would make Levi airborne with one punch if he ever saw him lay a hand on Historia again. While the outcome of such an action is obvious, the sentiment was very sweet.
While it happens in the midst of a tragic moment, Chapter 58 has a woman preparing to shoot Jean, to which the one panically yelling his name is Mikasa. For someone who's barely appeared to acknowledge his existence, it's nice to see proof that she does care about him and reacts frantically when it appears he's about to be killed.
Hitch turning out to be nicer than she initially appeared in Chapter 59, being genuinly upset over Annie's disappearance, and fighting to save Marlowe rather than running away when she thinks he's in danger.
In ACWNR. When meeting Levi, Isabel, and Farlan for the first time Hange tells them they were amazing taking down their first Titan and how “it was sincerely awe inspiring”. This meeting leaves an impression on the trio, as Farlan later points out that even Levi was beginning to get attached to the other members in the legion. It’s fitting that this chapter is called “the Heart”.
The trio's friendship in general is this. Even sweeter is that they don't act so much as friends as they do siblings.