For a kids show, MLP can really pull on your heartstrings. Here is a list of some of the most emotional scenes I have seen on this show.
Friendship is Magic Part 2: When Celestia and Luna are reunited
Winter Wrap-Up: When Twilight runs away crying after Applejack yells at her
A Bird in the Hoof: When Fluttershy bursts into tears when Philomena's ashes fall into her hooves
Owls Well That Ends Well: When Spike gets all teary eyed and thinks that Twilight doesn't love him anymore
Party of One: When Pinkie's hair deflates
Return of Harmony Part 2: When Twilight's tears form a broken heart
Sisterhooves Social: When Rarity sees Sweetie Belle's drawing
Secret of my Excess: When Spike is about to admit to Rarity that he has a crush on her, but she stops him and smiles at him
Baby Cakes: When the twins say Pinkie's name
The Last Roundup: When Big Mac starts crying and Fluttershy's line, "If you don't come back, we won't be able to fix the hole in our hearts"
The Super Speedy Cider Squeezy 6000: When Applejack is about to leave
Putting Your Hoof Down: When Fluttershy makes Pinkie Pie and Rarity cry and she discovers that she is a 'monster'
Dragon Quest: Spike's line, "I wonder if dragons cry"
Hurricane Fluttershy: Fluttershy's big crying scene
Ponyville Confidential: When everyone in town shuns the CMC
A Canterlot Wedding Part 1: When everyone scolds Twilight after she accuses Cadance of being evil and the BBBFF reprise
The Crystal Empire part 2: When Twilight is in her fear vision and Celestia is telling her that she failed, and after Spike sees his vision of Twilight sending him away and Twilight tells him that it will never happen
One Bad Apple: The line: Scootaloo: We are not babies. Sweetie Belle: Then why do I feel like crying. And when Sweetie Belle bursts into tears
Magic Duel: When Twilight's hoof and Spike's claw touch each other's in the dome
If you think I missed any, please reply back.