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.
 * "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 is definitely a qualifier here.

A Petty Nuzlocke Challenge:

 * Watch.
 * Spuds and Barb
 * 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
 * And so it ends. (watch the videos!)
 * The Christmas strip.

Sanguine Sapphire

 * Roxanne visiting May after their battle resulted in, and the exchange between them that helps May come to terms with what happened. Given how gym leaders who   are generally depicted, the compassion and caring she shows is really refreshing to see, as is May.

Sparradile's Nuzlocke Challenge:

 * Pepsi, after being raised into a Nidoking, finally has to admit to Chan that . Chan replies that he's never been anything but helpful to the party, and all this means is that she can.

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.

Kynim's Nuzlocke Challenges:

 * YMMV, but Fantina's "shape up" lecture to Kynim after the latter's pyrrhic victory at Hearthome Gym, along with, was quite touching in a tough-love kind of way.
 * In White version,
 * 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.