Heartwarming: It's A Dangerous Business, Going Out Your Door
The moments after the avalanche, where Rarity and Applejack help calm down Rainbow Dash, who's having a very big Heroic BSOD at being unable to see the sky in addition to being in a confined space.
Rarity and Rainbow Dash's discussion before going out to herd the konagas, where they reveal how much each has grown closer to the other, and Rainbow tells Rarity to call her "Dash," like all her closest friends (except Applejack, for some reason).
When Applejack stands firm in front of the World Snake, she draws upon the love of everyone she knows. Her friends, her family, the ponies they've met along the way, all of them give her magic strength as if they're standing right with her, and make her unmoveable.
When the World Snake had all three heroes in its coils and they simply prepared for death. What made this a CMOH was that each of them embraced and reflected that their friendship had indeed become something far deeper over their journey. Lastly, hearing Rainbow Dash actually say "I love you." and NOT mean it in the romantic sense brings a meta sense of tragic irony that's almost heartbreakingly beautiful!
The informal sequel, "A Day for Spike and Twilight" is mostly a CMOH in its entirety, but primarily the end, where Spike admits he views Twilight as a mother figure, and she realizes she feels the same connection towards him. It's a definite WAFF fic.
Spike: I'll never know the dragon who laid my egg. But I know the pony who's my mother.