A little boy sees through Jack's Paper-Thin Disguise and says that even though Jack lost to Yusei and everyone else thinks he's a loser now, he's still Jack's biggest fan and knows he'll win back the title someday.
Jack realizes that he took the easy way to being champion and now that he's lost he has nothing, no fans and no friends. Carly encourages him saying he can still make things up with his friends and be better because of it. Jack then has an Imagine Spot of returning to his old friends and all of them happily greeting him, including Yusei.
Nervin: Hey there Jack!
Tank: Hey pal!
Yusei: What's up?
Ruka:I don't care if you're not a Signer, you're my brother, and that makes you my hero.
The warm fuzzies are reciprocated later, in episode 78:
Rua: I'm not a Signer, but Ruka, who bears the mark of a Signer, is my pride!
Also doubles as a CMoA for Rua, who takes Luciano's plans to steal Ancient Fairy Dragon, which he'd already snagged, and completely derails them in a single move. Nearly getting killed for it if not for intervention by the Crimson Dragon, but still, to take someone who'd been laughing at him and his sister the whole Duel and render him completely pissed off at him in the blink of an eye is pretty damned impressive!
The aftermath of the Team Taiyo duel counts too.
The fallout from Rua becoming a Signer and getting Life Stream Dragon. Ruka recovers and Rua says "What a surprise, huh?" Ruka, being Ruka, says something to the effect of "I'm not surprised. You're my brother and I know you'll always protect me." The exchange left both of the twins in tears and probably would have brought a tear to Jack Atlas' eye. If Jack Atlas cried.
Rua, struggling to accept the possibility of Sherry's prediction that Yusei will die if he heads to the Ark Cradle breaks down in a fit of sobs, which then upsets Ruka. Yusei kneels down in front of them and they both jump into his arms and shake so hard from their crying that they manage to make his body shudder with him.
Something about the scene where we first see Yusei and Crow together, meeting for the first time in presumably years, always makes me feel warm and fuzzy inside.
All the prisoners in the detention center giving Yusei their cards for his duel with the warden.
The fact that Yusei's deck is made up of cards that are from all of the inmates that Armstrong was pushing around. These cards held a lot of importance to those people, so seeing Yusei basically using the strength of the people there is rather sweet of them. It shows that not all inmates in a prison are bad people.
Yusei's encounter with the spirit of his father in some sort of Momentum limbo after his duel with Rudger.
If the scene where Crow tries to cheer up Akiza after her loss to Andore in her first official Riding Duel by bringing her a cup of coffee didn't at least have you crack a smile, you DO NOT HAVE A SOUL. Double goes for the scene earlier on, When Hideo, her dad who previously had a strained relationship with her, waves a large "IZAYOI" Banner to rally her, all while shouting boisterous words of encouragement
This may only apply to those who ship Jack and Carly, but episode 59 is practically an episode of heartwarming. Because, y'know, Jack confesses to Carly, which gives him the power to use the Deus ex Machina dragon, Carly forces the duel into her loss so Jack won't die along with her, and that hug...
Yusei: "Everyone, I've come back."
Almost everything in episode 154.
The last time Yusei's father saves him. That made this Troper really happy.
Akiza and Yusei's final moment in Episode 154. (This doubled as a Tear Jerker moment for this Troper, because at that moment, it hit her that Yu-Gi-Oh! 5D's was over.)