Fluttershy embracing Firefly and saying she holds no grudges against her What the Hell, Hero? speech in chapter 3, after the latter apologized for her behavior.
The beginning of chapter 4, where Dinky shows Derpy a hoof-drawn picture of them with the words "I love you, mommy!" on it.
In chapter 8, Rainbow Dash and the pegasi from Mirage squadron are comforting Firefly after she tells them about her Dark and Troubled Past.
Rainbow does it again in Chapter 16 after Firefly has a Freak Out due to hearing that Black Star felt really bad about killing her parents - he did it because it was an order he received.
This exchange between Firefly and Derpy in chapter 9:
Firefly: I was wondering... why are you cross-eyed? Dont you have a problem with that?
Derpy: Its true that at times I feel a bit strange, but my eyes had always been like this... ever since... since Dinky appeared in my life. Maybe I had a normal sight before, but I cant remember that. I got used to this situation, and she doesnt seem to complain, either.
Firefly: OK, but I still dont get it; cant you get eye surgery or something?
Derpy: No... its best to keep it that way.
Firefly: But... why...?
Derpy: One eye is there to watch over my daughter and see her grow. The other is to protect Equestria from danger and ensure that Dinky can live in it.
The conversation between Rainbow Dash and Firefly on the balcony during Pinkie Pie's party.
The second part of chapter 10 is this, doubling as a Tear Jerker. The ponies comfort Fluttershy, who was suffering from post-traumatic stress from killing a living being (a villainous being, but a living being nonetheless) when she was trying to save Cloud Kicker's life. When Celestia and Luna convince her that she wasn't actually directly responsible for Razor's death, she makes a Tearful Smile.
Moments later, when Firefly and the other pegasi, sans Rainbow Dash, are trying to leave the room and make Fluttershy stay with her friends, she stops them and says the following sentence:
Fluttershy: Please, stay with us, Firefly. After all, we are... friends.
The Mane Cast in chapter 13 where Twilight assures Rainbow they will always be there for her, no matter what happens. Followed by one of several Group Hugs in the story.
It receives a Call-Back in chapter 17 right before Twilight's group starts an assault meant to liberate Canterlot from the opressing griffon forces.
Despite chapter 15 being a massive Tear Jerker, it has some beautiful gems:
Lightning Bolt: We've been fighting in this war together and well remain together. No matter what happens, we will always be best friends. Nothing will ever change that.
Cloud Kicker: I know. Then... I will keep fighting, too... Oh, Lightning... *sniff* What would I... Where would I be without you?!
Lightning Bolt: And me? Remember, Cloud Kicker... you are free to cry whenever you feel sad. Its fine. My flank is always available. *smiles*
Fluttershy trying to cheer Shamrock up and keeping him company after he initially wanted to be alone. When he gets better, Shamrock refers to her as "an angel that became a pony".
By the end of the chapter, when Derpy offers Pipsqueak to take up residence with her and Dinky, since his parents were killed by griffins. In short, Dinky will be having a foster brother. Firefly's comment seals the touching atmosphere:
Firefly: However you might look for the ponies on the outside... I can tell that inside you have a great and powerful heart. Im glad to know youre a part of our team, Derpy.
In Chapter 19, after defeating him in a duel and before she comes back to help her friends, Black Star tells Firefly how much she grew in recent years and that her parents would be proud of her. He openly apologizes for what he did to her and Firefly thanks him for being sincere and for telling her important information about Fortress Intimidation.
Majority of the epilogue.
"My friends are my family..."
Ace Combat: Wings of Unity
Roughly the first half of chapter 1 is filled with those. The interactions between Rainbow Dash and Firefly, and later, between them and their friends as well, are nothing short of sweet.
Blackberry: I even met Fluttershy. Yes, the one from Mirage squadron. She was the one you wrote to me about in your last letter, right? I guess you were correct if anypony deserves to be called an angel, its definitely her.
Cloud Kicker's attempts to cheer Fluttershy up by the end of the chapter were pretty sweet, too. It shows that she cares for her friends very much.
In chapter 7, Rainbow Dash assuring Spitfire that she can count on her and the Mirage squadron anytime, anyplace, if the Wonderbolts would ever need help.
Their entire conversation over Firebolt's grave jumps between this and Tear Jerker. It's simple, yet full of emotions and warm gestures.
A little bonding moment by the end of chapter 9 between Rainbow Dash and Medley.
Chapter 10a has several involving two Exile Pegasi, Bolt Burst and Pearl Eyes. The two are very much in love, and Bolt was willing to take on Flare Star all by himself, just to keep Pearl Eyes safe (and he even comes out alive!) Mooks they may be, but their moments together are still touching.
By the end of chapter 10b, Firecracker Burst apologizes to Short Circuit for harrasing her verbally earlier, saying she probably saved her life by leading the attack on the Exile camp. Short Circuit replies that she would never leave a friendly behind and adds that she wants to stick to that, which prompts Firecracker to call her by her nickname, "Bertz", which she took from her older brother who died in Operation: Valkyrie in Gryphon Wings.
Through the entire chapter 11a, Tornado Swirl and Overdrive remain unseperable. They are supporting each other and are even being fully prepared to die in battle after Orgoi traps them in an icy prison. Their conversation in hospital after the operation is quite touching, too. It all goes to show just how much those two ponies love each other.
By the end of Chapter 15, all ponies from Mirage squadron are distressed over Rainbow Dash's disappearance after her fight with the Reapers, with Medley accusing Firefly of leaving Rainbow to die. While everypony leave the main room in their base, Lightning Bolt stays to calm Cloud Kicker down, when she worries that their team is "falling apart". Lightning assures her that she will remain by her friend's side no matter what.
Fluttershy goes to calm Medley down in a truly motherly way. Her warm words and a soothing lullaby manage to calm Medley's anger in the sweetest way possible. Fluttershy also says that she believes Rainbow is alive because of their connection to the Elements of Harmony and how she senses her presence. However, it's a lie.
The ending to chapter 16, where Derpy converses with a sickened Dinky. She explains her reckless actions by trying to save her friends, as well as her mother. Derpy acknowledges it, says she's not angry at her daughter but very proud instead.