Nuzlocke Comics/Heartwarming

Main Series:

• "Doc... nobody's dragging us."
• "...don't forget... It's just a title, Ruby."
• Juliet dies shortly after being caught, much to Sawyer's dismay. As a result, he refuses to be used in the next gym. Ruby states he wasn't going to use him anyway, as it was the electric gym. After he loses his pokemon but ultimately wins the gym, he finds Sawyer eagerly awaiting him outside. Their faces are too much.
• Meowth: "If 'it' ended... What are we doing right now? You didn't screw up, master... You believed in me."
• Oshawott's reaction to getting picked is so sweet, even if the feeling isn't mutual for Ruby.
• "no matter what's happened... I still believe... it happened for a reason."

Freddy's Nuzlocke Adventures:

• FREDDY!!!
• All the friends you've ever lost must be at peace.

landwalker's Nuzlocke:

• Regardless of how it ended, Rikishi popping out of his Pokeball of his own free will to take a lethal Hyper Beam for Ninio is definitely a qualifier here.

A Petty Nuzlocke Challenge:

• Watch.
• Spuds and Barb adopt a Togepi egg at long last, since Nidoqueen's inability to breed meant they couldn't have kids of their own.
• Pretty much everything involving Spuds and Barb, save for maybe some of their more shallow interactions early on. Special note goes to the end of the Christmas Episode and their aforementioned egg adoption.
• And so it ends. (watch the videos!)
• The Christmas strip.

Sanguine Sapphire

• Roxanne visiting May after their battle resulted in Marie and Claire's deaths, and the exchange between them that helps May come to terms with what happened. Given how gym leaders who kill somebody's starter are generally depicted, the compassion and caring she shows is really refreshing to see, as is May admitting her own arrogance played a role.

Sparradile's Nuzlocke Challenge:

• Pepsi, after being raised into a Nidoking, finally has to admit to Chan that he's not poisonous. Chan replies that he's never been anything but helpful to the party, and all this means is that she can hug him without risk of being poisoned by his spikes.

Paratroop's Nuzlocke Challenge:

• Paratroop writes a postcard to her mother, who has difficulty with going outside, and mentions a gift she left for her in the garden. the gift is a picture of Para and her parents at a picnic signed, "Remember us being outside, I missed that-P"

Kynim's Nuzlocke Challenges:

• YMMV, but Fantina's "shape up" lecture to Kynim after the latter's pyrrhic victory at Hearthome Gym, along with providing a doll to symbolically bury Tyrus, was quite touching in a tough-love kind of way.
• In White version, Elesa taking Bianca to talk to Social Services about her father's abusive behavior.
• Jordan and Mimi's blossoming romance can almost always lead to a big case of d'aww.

Other:

• Challenges that end up in the Pokemon Tower at Lavender Town or Mt. Pyre almost always have scenes that involve reuniting with the ghosts of previous party members. Manly Tears ensue.
• This moment. CMOH, Crowning Moment of Awesome, and Tear Jerker all coming together at once.