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.
This exchange between Firefly and Derpy in chapter 9:
Firefly: I was wondering... why are you cross-eyed? Donít you have a problem with that?
Derpy: Itís 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 canít remember that. I got used to this situation, and she doesnít seem to complain, either.
Firefly: OK, but I still donít get it; canít you get eye surgery or something?
Derpy: No... itís 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.
Despite chapter 15 being a massive Tear Jerker, it has some beautiful gems:
Lightning Bolt: We've been fighting in this war together and weíll 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. Itís 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. Iím glad to know youíre a part of our team, Derpy.
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 correctÖ if anypony deserves to be called an angel, itís 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.