Just about everything that Dinky Doo does, but especially Chapter 5, "Catharsis," of Family Matters, when we finally get to see Sparkler's side of things, and when she and Dinky just break down in front of each other and Dinky ends up consoling her older half-sister.
And chapter six, where Sparkler and Ditzy begin reconciliation.
In Chapter 3 of Family Matters, Diamond Tiara actually compliments Dinky on all the hard work she did to earn money for her mother's birthday present. Sure, she tells her not to let anypony else know about it, but it's still a nice sentiment, especially if one sees it as a sign her father really is managing to teach his Spoiled Little Princess the value of hard work in some way...
Trixie not wanting to interrupt when Ditzy and Dinky are having a moment of peace in The Night After
The various ponies Carrot Top had helped out returning the favor to her in Carrot Top Season.
During Symphony for Moon and Sun, Lyra's absolute refusal to abandon her friend Octavia, despite her previous betrayal.
As an extension of that, while Octavia is being mind controlled into feeling worthless, what snaps her out of it is the mere idea that Lyra would abandon her. She knows that would never happen.
In A Hard Bargain, after all has been said and done, Trixie goes over to Ditzy's with a tub of ice cream for them to share. During their conversation, Ditzy reveals that she feels guilt over punching Trixie when she was trying to help her, as well as losing it at the train station with Parley during her High-Altitude Interrogation with him. When she dropped him, she actually didn't know if she would be able to catch him before he hit the ground.
Ditzy Doo: I took him up there knowing that if I let go he would most likely die before I could get to him… and I didn’t care. I was so angry…I didn’t care about what I did. I just wanted to hurt him. What sort pony does that make me?
Trixie Lulamoon: It makes you a good pony and a great mother that’s had a really bad day. You know, my mother once told me that if you weren’t willing to shed blood for the sake of your children, you didn’t have the right to call yourself a parent.
Luna comforting a crying Cadence in An Early Reunion. Becomes even more Heartwarming in Hindsight when you read the following chapter.
Cheerilee singing Ditzy a lullaby in Through the Fire and Flames after the poor girl blamed herself for letting her claustrophobia cause a setback to rescuing Trixie.
Scootaloo getting to meet members of the Guard who knew her mother in Foaling Around.
Luna and Trixie comforting each other in At the Grand Galloping Gala after the latter's Heroic BSOD. As rocky as their relationship is sometimes, it shows just how much they actually care about each other.
Later, the other Elements of Harmony all agree to help Trixie with her plan to force reform on the Night Court, even though it's made clear that what she intends to do is very illegal. Whatever the personal consequences will be for them, they barely hesitate to go to the firewall for each other and for the good of Equestria.
Lunaverse!Luna and Maneverse!Celestia wing-hugging in Crisis On Two Equestrias. Doubles as Tear Jerker with this line, though:
Celestia looked uncomfortable as she managed to get herself into a sitting position. “Princess Luna,” she said. “I am not your sister.”
“I know…” Luna breathed, not moving. “I know, but please, just for a moment…let me pretend…”
The Story entitled Pinkie and Bluie featuring Lunaverse's Pinkie Pie and Blueblood (you read that right). Its rather sweet for Blueblood to realize that Pinkie, out of all the others he's been with, is the one he wants to be with cause she makes him happy and makes him believe that he can be a better pony.
Likewise it's sequel, Pinkie and Bluie Twoie - A Pinkie and Bluie Hearth's Warming. It takes place on their first Hearth's Warming as a couple, and involves each of them, on their own, deciding to help the other reconnect with their semi-estranged family.
It's a small one, but in chapter 6 of The Return of Tambelon Trixie starts to briefly empathizing Corona a little after she told them her view of what happened 1000 years ago.
Also, you will notice that Corona is becoming slightly more lucid as time passes.
After they defeat Grogar, Luna lets Celestia raise the sun.
More or less all chapter 5 of A Concert for Ponyville Fluttershy and Octavia bond and the latter recognises the former works hard for her animals. Trixie seems to truly understand Fluttershy and helps her out of the goodness of her heart rather than to prove she's a good friend. Soft Hoof's story about her dog saving her life and then Fluttershy's aunt being so very proud of her niece. It's just one of the sweetest parts of the whole lunaverse so far.
The Flashback in Chapter 6 as well with Luna and Celestia, seeing the two act like sisters before she went berserk.
The last chapter of Magic Tutor, both halves. In the first half, Twilight is formally welcomed to Ponyville, and starts to make friends with the ponies there, including Applejack, Rainbow Dash, and Rarity. In the second half, the foals that Trixie and Twilight had been tutoring have a school recess and and basically all act adorable
Greengrass and Notary being reunited at the end of Just Us Little Ponies. They both care so deeply for each other, and they went through so much while separated, that the reunion is absolutely heartwarming.