A big general one: Anybody who has seen the original My Little Pony cartoon knows the horrors the ponies had to deal with. Megan decided that enough was enough, and poured her heart and soul into founding Equestria, so that her friends would know peace.
Even though Blueblood has been shown to be a self-importantJerkass in the show, his blushing while Megan hugs his neck is all kinds of adorable.
Any of Megan's reunions with people from the old days.
Megan and Crew finally reunited with Luna and Celestia. To quote directly from Celestia, "I'm so…happy!"
Megan's graceful greeting to the princess ponies.
Megan and crew finally recognize that their little Spike has become king of the dragons.
Megan, Sparkling Dawn, and Blazing Day entering Morning Glory's mind with Twilight Sparkle's help to break her discording, and Morning Glory catching up with her family afterwards.
Plenty of the flashback moments. One good one would be Rosedust agreeing to join the Equestrian Alliance, after Megan has helped deliver Morning Glory's son Blazing Day.
Another one is a young Luna comforting Blueblood I over Princess Platinum being permanently frozen.
Morning Glory's family after her discording is reversed thanking Trixie for her kindness towards Morning Glory earlier.
The flashback to Cadence's "birth"; specifically how it was the Heart's reaction to Celestia's loneliness following Luna's banishment.
Twilight's reunion with Shining Armor and Cadence, and her joy at getting to introduce them to her friends.
Her reaction to finding out they're getting married, once the humor wears off.
Megan's flashback to the original Grand Galloping Gala, which was little more than a "glorified picnic" between her, Danny, Molly, and their friends.
Big Mac and Fluttershy's picnic, and them agreeing to have another one.
Megan, Danny, and Molly seeing the statues of their old friends (like Surprise, Heart Throb, etc.), thanking them for everything and misses them. Which doubles as a Tear Jerker, since they only wish they could tell them in person (or pony) and they've been dead for almost 1,500 years. Even Twilight Sparkle spoke to the statue of her ancestor, the original Twilight, thanking her for all that she's done for Equestria.
The video of Megan and her friends at the original Applejack's birthday party. The Apple siblings view it, and are moved to tears.
Celestia promising Applejack she'll bring the tape to the next Apple family reunion.
The next time Applejack and Megan talk, Megan assures her that the first Applejack would be proud to call her family.
In a side story, Dinky and Sparkler have convinced the CMC to help them find a few friends of their father using his time machine. What time machine? A certain blue box. All because he's missing friends like the Brigadier and Sarah Jane. They also find Ace, Captain Jack Harkness, and most importantly, Susan Foreman, AKA, the Doctor's Granddaughter.
Scootaloo invites Danielle and Michelle to join the CMC.
Thanks to the presence of the Richards family, everyone got a happier ending to the Grand Galloping Gala. AJ got her endorsement, Rainbow got some fun bonding time with Spike, Fluttershy got a date with Big Mac (preventing her meltdown), Pinkie got to play with the kids, Twilight got some fun time with Celestia and Luna, and the princesses got a way to connect with their people. True, Rarity still went away disappointed with Blueblood, but for much more adult reasons. All in all, things went far better overall than the old universe.
Luna and Celestia have fond memories of watching Mr. Roger's Neighborhood as fillies.
Luna and Celestia both assure Megan that even though the dangers are past, she is still welcome to help in Equestria however she sees fit.
After the Elements of Harmony destroy Tirac, they allow Megan and her siblings to meet the spirits of their deceased G1 friends, finally giving them closure.