Heartwarming: My Little Pony: Friendship Is Magic (IDW)
During the climax of issue 4, the mane 6 and the Crusaders all talk about how their bonds of friendship and love give them the strength and conviction to do anything.
During the fight, Sweetie Belle and Scootaloo sing Twilight's praises as she faces Chrysalis alone. Sweetie Belle thinks Twilight is the best unicorn there is, and Scoots wants to be just like her. Considering how much the two idolize Rarity and Rainbow Dash respectively, that's saying a lot.
At one point in issue #4, Scootaloo comments on the lack of having a big sister. Later, we see Rainbow helping to rescue Scoots in the same vein as Applejack does with Apple Bloom, and Rarity with Sweetie Belle. The precursor of Scootalove from "Sleeping in Ponyville" is evident.
After Twilight finally defeats Chrysalis, the CMC are rescued, and everypony meets Celestia and Spike outside, it's really heartwarming to see them all reunited around the campfire, finally safe after all they had to go through, especially when you consider that just a moment earlier Twilight was a hair's breadth from unwillingly turning into a monster that would destroy her own friends. A happy ending well deserved, indeed.
Finally rescued from the kidnapping, Apple Bloom and Sweetie Belle can be seen sleeping snuggled against their big sisters by the campfire. At first, this troper thought that Scootaloo had just been completely shafted from the panel, as she wasn't with Rainbow Dash or seemingly anyone else. But then...
In Issue #6, Twilight catching the Fire Ruby Spike dropped as they were falling to the moon, even though a moment before she was telling him to forget about it.
Spike: Aw, Twilight, you're the best!
When the Nightmare Forces try to convince Luna to sacrifice herself to save the others, the Mane Five quickly butt in and tell the Nightmare Forces that they're not going to take any more of their friends.
Luna: I'm your friend?
Issue #7: Even though it was cruely subverted seconds later, it's still pretty heartwarming to see Spike coming close to telling Rarity he loves her. She's more than just a crush to him now.
Issue #8: Twilight's reaction to discovering Spike survived what happened in the previous issue.
Everypony convincing Luna that her fight against the Nightmare Forces isn't her burden alone. Amongst these ponies is Trixie, who knows full well the regret Luna is feeling. Considering the number of fanfics where their roles are reversed, it's surprising to see it the other way around in an official work.
Spike delivering the final lines prior to Rarity's liberation from Nightmare Rarity's grip. He gets extra points since the destroyed Fire Ruby repairs itself while Spike tells Rarity that she's everything for him and asks her to please come back home. After that, there's the final scene.
Though #9 and #10 are mostly slapstick and making a Butt Monkey out of Big Mac, the end has Zecora convince a grumpy Big Mac that the fair had some high points in addition to being a massive obstacle. Big Mac thus decides to give up on the nails and enjoy himself.
Cheerilie affectionately greets him, showing that they've apparently remained good friends since Hearts and Hooves Day.
He also gets a kiss from a princess!
Issue #11 gives us little filly Vinyl Scratch getting her cutie mark while standing on her brother's back watching Shining and his friends perform. She has the most adorable smile on her face.
Issue #12 when Shining Armor finally stands up to Buck's arrogance and finds out, after all the time when Buck has been making him feeling so alone, that the rest of the school hates the Jerk Jock too and admires Shining far more.
While Shining's nervous greeting to Cadance as he's leaving for his flugelhorn recital is played for laughs, issue #12 makes it heartwarming, by revealing that Cadance found his nervousness to be absolutely adorable.
Shining Armor & Cadance's first kiss at the end of their flashback.
The end of "Neigh Anything." Cadance ends her account saying that she and Shining lived Happily Ever After. Shining corrects her, saying that they are still living happily ever after.
The resolution of the bookworm problem: It turns out he's just upset that bookworms are never the heroes in any of the stories he comes across, and Twilight convinces him to become one himself by putting everything back to normal.
When Celestia and Luna get some private time, Celestia admits the reason she kept her time in parallel universes a secret is that she's ashamed of her youthful indiscretions. Luna responds by nuzzling her and telling her she doesn't have to be perfect just because she's a princess.
In the mirror world, Sombra gets one when he firmly says "No harm may come to her. I love her." regarding Celestia after it's discovered that fighting Evil!Celestia and Evil!Luna in any direct fashion will hurt the good versions. He's the one apparently in the most danger from whatever they've got planned, but his only concern is making sure that Celestia is safe.
YMMV (depending on whether you like their pairing or not), but Celestia's flashback in issue 19 to when she and the Mirror World's version of King Sombra are rubbing noses, followed by their exchange in the following panel:
Celestia: I have to go.
Mirror World Sombra: I wish you didn't.
Celestia: I know.
Sombra turning down a deal that could allow him and Celestia to be together, because he knows it would leave Celestia's world at the mercy of her evil counterpart.
Main!Luna forgiving her with a little hip bump and another joke about perfection. Adorable
A flashback in Issue 20 shows that despite chewing her out and sealing off the mirror portal, Starswirl ended up forgiving Celestia, and admitted that he sympathized with her on the matter, but had to make a hard decision for the greater good.
Mirror!Sombra catching Mirror!Luna after Mirror!Celestia attacks her. Likewise, Main!Celestia's concern for her sister after the attack's effects hit her.
Celestia being perfectly willing to become sealed in crystal in order to stop Mirror Celestia. In what she thinks will her last conversation with her student, she tells Twilight how proud she is of her.
Mirror!Sombra making a Heroic Sacrifice to save Main!Celestia and both Equestrias, using the Elements to absorb the evil magic of Mirror!Celestia and Luna into himself to restore the balance between the worlds. He knows that he'll be warped into a malevolent version of himself, akin to the main universe's version of King Sombra, but he goes through with it anyway. All so his beloved won't have to sacrifice herself.
The last panels show Celestia and Sombra bidding farewell to one another in a Bittersweet Ending...and yet, as corrupted and dark as he's now become, the sight of Sombra shedding a tear shows that some part of him still loves Celestia, and thus may not be as irredeemable as his main universe counterpart..
Trixie referring to the gang as friends, and assuring Chief Stablemaker that he can trust them.
Trixie trying to become a better mare and help the police catch Rough Diamond. It turns into a tearjerker when Rough Diamond turns it into a Frame-Up though
Applejack and the others being willing to give Trixie the benefit of the doubt.
Babs relating to Trixie about how they're both former bullies. Trixie is so touched that her eyes glisten up and she sweeps the filly into a bear hug!