In the first chapter, when Celestia is affectionately drying off Luna after she gets soaked by a fire sprinkler in the aforementioned Microwave Incident.
Actually, Celestia's gentle and kind-hearted treatment of Luna in general. While she does engage in some teasing, it's obvious that Celestia genuinely cares about her little sister.
Luna's whole interaction with Applebloom is D'aww worthy from start to finish.
Three from(ironically enough) Luna Vs. Lodging Part 3:
Big Mac has Luna take a look at the skyline for the first time since she returned. When she does she sees how beautiful it is and how many lights are around, showing how many ponies now appreciate the night she brings after all these years.
Hoyden making up with Sundance
A very small one but after Derpy and The Doctor Return the Abacus and The Doctor thanks her before running off, Derpy stops to give Luna a peck on the cheek before leaving. Daw.
Try not to smile at the picture of Pinkie Pie and Luna riding in the pedal copter together at the end of Vs Ponyville part 3.
The whole relationship between Hoyden, Sundance, and Luna is equal parts hilarious and heartwarming. Hoyden and Sundance are very much the odd couple, but it's sweet how the pony-equivalent of Johnny Knoxville can get along with what can basically be referred to as a G1 pony. Luna's child-like innocence can sometimes make her seem like their own child, while other times, she's more like that goofy friend who always needs an extra hand with whatever mess he made. All-in-all, they're the textbook example of a sitcom match up.
Luna having Twilight Sparkle help her raise the moon.
Luna writing a letter to Celestia in the vein of Twilight's letters, expressing acceptance of her own flaws after seeing how flawed the Mane Six are but knowing they're still a kind, generous, friendly group that have forgiven her for her sins as Nightmare Moon.
Luna vs Storytelling. "Here's to you... Whoever you were, you've still got her." Manly Tears.
Also, Luna's story in general. That pony was so determined, never gave up even when he was injured or starving, and he finally did it, all for her. Then it comes into Tear Jerker territory when we find out he sacrificed himself to hold back the Smooze.
A sly one early in "Ponies in Space": Luna mentions the "Province of Epona". Back in "Luna vs. the Facts of Life", Celestia claimed Epona was one of her children. If she wasn't lying, that means she named part of Equestria after her daughter.
Or named her daughter after the province.
In "Luna vs. the Dreamlands, part 2:"
Luna willing to enter Discord's dreamscape and presumably risk herself to ensure he will not harm another pony. Further when you realize that this action was probably undertaken when Luna learned that Sundance was pregnant.
Also kind of heartwarming to learn that many pregnant mares are planning to name their children after Twilight Sparkle. They seem not to have forgotten the pony who saved Equestria.