One from the pilot towards the end of the "Dancing on Air" song. Megan has spent most of the flight doubting that she could be of any help despite Firefly's assurances. But Firefly doesn't give up on her, and after she tries one more time Megan is at last convinced. Her voice fills with hope and delight as she joins Firefly in the final repeat of the chorus.
Twilight comforting Ember and telling her she'll grow up to her own special pony. Admit it, its adorable.
After Tirac is killed, Scorpan is restored to his original human form.
Catrina and Rep in the party of the second special. Particularly wonderful when you consider she was an homicidal maniac just minutes before.
Rep the entire time. Though nobody tops Tirac/Tirek/whatever in terms of evil, Catrina was very much a Bad Boss, but Rep's Undying Loyalty to Catrina as she had been before the Psycho Serum never faltered. He took all manner of abuse from her as he tried to get her back to the way she had been. On top of that, despite his love for her, there's a limit to what he could stand by and see her do to innocents. This is what makes that final scene with them at the party so wonderful: Talking about having to Earn Your Happy Ending; but in the end, he earns one for everyone. All the risks and sacrifices won in the end.
Another layer to the party at the end: the ponies never knew the old Catrina, and mostly knew Rep as The Dragon. They were still willing to accept that it really was the Psycho Serum's fault and forgive.