When we find out what Kouji was doing on the day he went to the Digital World buying flowers for his step-mother and what he had intended to do call her "Mom" for the first time.
Kouichi, considering all that happened to him during the course of the series, we find out that unlike the other children, he is simply a spirit in the Digital World originally summoned by Cherubimon to do his bidding, and that he is near-death in the human world.
It's really the delivery that sells it. Episode 30 and 32 are pretty much the Wham Episodes here as they basically amount to establishing that Duskmon, the villain who had scared the living daylights out of Takuya and given him hallucinations and had practically beaten the five every time he met them was actually a lonely child who wanted very, very badly to meet the twin brother he never knew he had.
Bokomon and Neemon's last scene. Yeah, the comic relief duo actually have a sad last scene with Bokomon, out of nowhere, crying and begging the kids not to leave him so soon and Neemon for once pulling him back. Bokomon's final words are tearfully shouting out to the kids that he'll write down everything that they have done to save the Digital World so that generations of digimon will always know of them and all they went through as "the best friends a digimon could ever hope for." Aaaww...
The finale of Digimon Frontier. Say what you want about the series, the finale was well done, with the kids saving Kouichi at the last possible moment. And then the scenes of their lives afterwards, Takuya appreciating his family more, Kouji respecting his step-mother and giving her flowers for her birthday, Zoe/Izumi and JP/Junpei finding friendship, Tomoki/Tommy being friends with the boys who used to bully him, and Kouji meeting his birth mother again with Kouichi's help - not to mention all six friends in the ending shot promising to be friends forever...ugh. And to top it off, it looked like the franchise was done at time of the finale, so to see the animators pull of a great finale out of an uneven season was nothing short of amazing.
Ranamon's death. Seeing Kazemon know that she actually had a good heart deep down and only was evil because she was lonely, and wanting only to purify her....*Sniff!*