The method in which Kouji gets his first spirit in episode 2. Despite putting off an aura of "I don't care about anyone else.", the moment he realizes Tomoki/Tommy and Junpei/J.P. 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.
Episode 13, the loyalty between Sorcerymon and Seraphimon. They're not just a ruler and his servant, they're real friends.
Seraphimon: Dear brave Sorcerymon. You are a true friend. Thank you.
Junpei's/J.P.'s drive to get Izumi's/Zoe's spirit back for her is really, really sweet.
Episode 16 Zoe's sympathy for the Gomamon.
In episode 17, Tommy meets a Datamon. Datamon appears to be a jerk at first. However, when Arbormon tries to give him the camera he'd traded with the Toucanmon for the stolen D-Tectors he sees Tommy being compassionate to the Toucanmon, thanks to the camera recording it. So Datamon stands up to Arbormon and decides to not give him the D-Tectors. A much more sympathetic character than the original Datamon from Digimon Adventure, who was a selfish ungrateful jerk.
In another cameo, Zoe talks to a Gallantmon who note in the English dub at least even wishes he could be of more help.
Near the beginning of episode 20 "From Dawn To Duskmon", everyone is at first frightened of the Dark Continent. However, after they encounter some friendly Pipismon they all agree that some things about the Dark Continent are harmless and not as terrifying as they'd feared.
From episode 22, 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.
Episode 25, "The Dark Heart of Friendship". 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 "The Bully Pulpit", 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.
In episode 26 Zoe befriends a group of Honeybeemon who are attempting to capture her for Ranamon. All she does to win them over is show them some kindness, (and save them from their failed attempts to capture her). It doesn't take long for the three Honeybeemon to realize Zoe genuinely cares about them, while Ranamon only cares about herself.
Episode 31, after the kids finally get back together again Koji meets Patamon for the first time. Patamon introduces himself to Koji by happily leaping into his arms.
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.
In episode 33, Patamon comforts Kouichi by pointing out that the power of darkness doesn't necessarily have to be evil by nature.
Patamon: Darkness isn't a bad thing unless you choose to make it that way.
Ophanimon Taking the Bullet for Zoe when Cherubimon tried to take her D-Tector in "Takuya and Koji's Evolution Revolution".
Anytime that Koji and Koichi are hanging out is heartwarming when they're not being hammy about it.
Takuya: If we just keep believing in ourselves and going forward we will win!
In the episode "Glean Eggs And Scram", 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. These 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 their help, all four smile before they return to egg form.
After dying back in episode 13, Sorcerymon returns as a spirit in episode 44 to protect the kids from Dynastmon as he destroys Seraphimon's castle.
Koji's friendship with Gotsumon enables Gotsumon digivolve into Meteormon.
After Cherubimon's defeat, he's cured of Lucemon's corruption and sees the spirits of Seraphimon and Ophanimon. The two have no harsh words for him, but instead warmly beckon him to join them. In death, Cherubimon was able to be forgiven by his precious friends and it drives him to tears as the three Disappears into Light.
It's a very small moment near the end of the series but, seeing Patamon reunited with the rookie versions of Ophanimon and Cherubimon in episode 47 was a very heartwarming moment. The three don't remember their past lives as the Digimon Seraphim, and now are getting another shot at their friendship after it originally went so awry.
Late in the show ("The Brothers Yin and Yang"), 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.
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.
In the dub, Rika's voice comes across very sweetly when she's narrating. It sounds like her character development stuck.
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.