Yangus' backstory: He was a former bandit who'd tried to turn his life around but due to his apperance he was forced to go back to his old life of crime to survive. He then ran into The Hero and Co, demanding money to cross a bridge. When King Trode refused, Yangus attacked but ended up breaking part of the bridge and falling too, clinging to it for dear life. Despite having every reason to leave him, the Hero goes back to save him, earning Yangus' gratitude and service as a result.
Yangus's "Golden Oldies" super attack. Calling out to King Trode "Grandad", it's nice to know that the pair have been bonding all throughout out the game in spite of their normal interaction.
It's also shown earlier in the game. After cheering up the King of Ascantha, King Trode is moping about not having been able to enjoy the same feast and being stuck outside town in the wagon. Who says he knows how he feels and immediately suggests going to Pickham just so the guy can at least have the opportunity to go to a tavern? Yangus.
Felix's sidequest, Baumren's message to Felix specially. "Tell him that I... Baumren... owe a lifetime of happiness entirely to him."
Wrapping up the Cash and Carrie sidequest, where the two siblings finally put aside their petty feud to inherit the Golding fortune together. The portrait of Golding in the mansion even smiles.
In the 3DS version, they even Captain their own Monster team together in the new Rank X at the arena.
The story of King Pavan and his queen, particularly after you play the harp for him. Sniff.
Empyrea's grief at losing her baby turns to joy when you find out that the chick's spirit was too strong to be destroyed. Then despite his mothers protests he chooses to become a party power-up! That little guy's quite the badass, and he's just a baby!
The flashback to when Medea first met the hero: Despite being in a Heroic B.S.O.D. over the loss of her mother and wandering the forest in her grief, she drops everything after following Munchie to find the hero unconscious in a clearing, gets her father to take him back to the castle, and stays by his side until he wakes up.
When despite Marcello hating Angelo's guts for like EVER, Angelo still saves his life all because of a few moments of kindness.
Both the normal and unlockable ending's are very sweet. They both have the hero marrying Medea.
The additional scenes in the 3DS version that lead to opening the Jessica ending: she and her mother finally reach an understanding, her mother gives Alistair's armor to the hero because that's what Alistair would have wanted, then Jessica and the hero pray at Alistair's grave together.
The Golden Ending where the hero marries Jessica too, especially when her mother is there to escort her down the aisle with Bangerz and Mash attending too as it's revealed King Trode arranged to bring them halfway across the world from Alexandria overnight. King Clavius also publicly recognizes the hero as his nephew (especially poignant after giving him a What the Hell, Hero? speech the night before). And the whole thing culminates at the very end with Jessica calling the hero "Hubby."