It may just be me but Gravelyn mentions that Chuckles was her own creation and how her daddy Sepulchure was proud of her making her very first minion was very sweet. Especially when Chuckles returns, saves his mistress AND gets a promotion to boot.
The fact that Chuckles seemed to be seen as a right hand man for Sepulchure, suggesting that Seppy is often accompanied by Chuckles into battle. The implication being that Sepulchure keeps chuckles around as a reminder of his daughter's achievement.
Any of the wedding events are like this. This includes:
The first ever wedding between two characters.
Cysero's wedding and Nursey explaining that she loves her husband for who he is.
Nythera and Ryuuji's wedding, especially when Ryuuji would give his own magic to power Nythera up and used remnants of their three trials to make a ring for her.
Ai No Miko reunited with her father once the player defeats Kitsune.
The first part of the 2011 Frostval Event has you bringing the spirit of Frostval to Gravelyn. And it is adorable.
The ending of the 2012 Heroes' Heart Day event. In the end, you help Romeo and Juliet get a truly happy ending.
The ending of the 2013 Heroes' Heart Day event, which has Princess Brittany finding love in Lord Brentan, Swordhaven's new War General.
A somewhat warped example, but when Mirror Drakath appears in front of the Chaotic twins mirror Xang anounces she doesen't want to go back, and Xing immediately states that "I won't let you take my sister!". Admittedly they technically aren't really sisters, and they both actually abandoned their real sister but the fact that they're that close comes across as pretty heartwarming. And of course that would imply that the two good Sisters in the mirror realm are happy together as well.