The method in which Kouji gets his first spirit. Despite putting off an aura of "I don't care about anyone else.", the moment he realizes Tomoki and Junpei are in legitimate danger, he jumps down in front of them to fight off a creature at least ten times his size. It's hard not to draw the comparison to Takuya's initial run (protecting some kids he's just met) as proof that their eventual close friendship makes perfect sense.
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 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.
The series' second Japanese ending theme, "An Endless Tale." Its lyrics are very sweet-sounding, and the animation at one point shows the kids all holding hands with their respective Human Hybrid forms.
When Takuya realizes that running from his mistakes solves nothing and decides to return to the Digital World, the dark Trailmon that brought him back to the human world actually sounds proud of him.
It's refreshing that unlike the cases of Ken and Impmon, Kouichi is immediately forgiven for what he did under the influence of the corrupted dark spirits by the entire group, despite the fact that they affected him in the first place because his anger/negative emotions gave them the power they needed.
Late in the show, Kouji and Kouichi are talking by themselves and Kouichi brings up their mother, using the word "mom". Kouji informs him that that title has been given to his stepmother. Kouichi immediately looks sad but then Kouji tells him he wants to hear about "our mother". Not only does this scene reinforce the earlier flashback that showed us Kouji was planning on making amends with his stepmother right before the whole "went to the Digital World" thing but that he has no resentment towards his biological mother and wants her to be a part of his life just as much as he wants his brother to be.
During the credits of the Short Anime Movie, we see that the mural of Ornismon, AncientGreymon and AncientGarurumon has been added to. Bearmon added drawings of the heroes, Dinohyumon, and Grizzmon. Kotemon, who got himself turned into a Digi-Egg trying to stop Ornismon, shows up good as new just as Bearmon completes the mural and Bearmon runs over to him, revealing one last section of the new mural. The last drawing? Bearmon and Kotemon together.