When Tommy is all alone inside Sakkakumon. He remembers what his big brother tried to tell him about self reliance. In the end he figures out what his brother was trying to tell him and is the better for it.
In another episode focused on him, he encounters the bullies that pushed him on the train. Long story short, they've made good by the end of the second part of the episode.
Anytime that Koji and Koichi are hanging out is heartwarming when they're not being hammy about it.
In the dub, Rika's voice comes across very sweetly when she's narrating. It sounds like her character development stuck.
Junpei's drive to get Izumi's spirit back for her is really, really sweet.
It's a very small moment near the end of the series but, seeing Patamon reunited with the rookie versions of Ophanimon and Cherubimon was a very heartwarming moment.
In the episode where the kids try to save the Village of Beginning's (the place were all purified digimon eggs go to be reborn). When it looks like the Royal Knights will win again, four digi-eggs come to the aid of the Digi-Destined. This eggs contain the now purified Legendary Warriors Mercurimon, Ranamon, Grumblemon and Arbormon. Together, all ten Legendary Warriors unit and force Dynasmon and Crusadermon into submission long enough to save all the remaining digi-eggs. While the kids thank the four for there help, all four smile before they return to egg form.