Considering the absolute bastard he was as the Emperor (at the time, seeing his illusions of control broken down piece by piece gave off a definite sense of "Ha! You so deserved that!") it's amazing that most of the things Ken Ichijoji does afterwards bring tears to this troper's eyes, resulting in her being unable to watch the earlier season episodes anymore without feeling incredibly uneasy. From his first recognizing his own Mother after coming out of a not-at-all-Heroic-BSOD, to seeing his dead brother in an illusion caused by his own desire to see himself punished for his misdeeds, to Davis yelling that he's not alone anymore while he's struggling with the serious mental and physical pain of trying to close a Gateway to the Dark Ocean that's haunted him since he was seven... This guy really had to earn his happy ending.
Wormmon's death. It's just downright heartbreaking.
The scene where Ken goes into the Digital Nursery and all the Digimon start whining whenever he comes near them and he finds Wormmon's baby form and holds it in his arms and starts.....BAWLING his eyes out. Especially the flashback where he wishes his brother was gone and then he is.
Also his poor mother's reaction when he returned (briefly) to the Digital World and she thinks he's gone for good. Definitely Adult Fear.
The scene where Oikawa is harvesting the Dark Spore to inject it into kids he's tricked is hard to watch since we see Ken the closest to a total breakdown he had been at the point in the series since Wormmon's death.
Oikawa's backstory ( specially when he recalls when he was offered his Deal with the Deviland how, right before that, he's bawling in despair since his beloved friend Hiroki isn't there with him to see the Digital World they believed in as children) in Digimon Adventure 02
BlackWarGreymon's Heroic Sacrifice to save Cody's grandfather after finally realizing the true meaning of friendship, WarGreymon sounded like he was about to cry.
And Oikawa's death scene? Where, for the first time since his possession by Myotismon, he wakes up long enough to see the Digital World for the first time. Then he finally gets his partner Digimon, seconds before he dies, dissolving into energy and using that to heal the damage Myotismon did. Both Cody's plea for him to hang on, and his partner Digimon's line "Are you leaving now? But we've only just met!" are particularly effective.
Just the look in Oikawa's eyes when he finally makes it to the digital world and sees his long lost Digimon partner for the first time in years is moving enough, even before he dies and restores the digital world.
Mummymon's Villainous Breakdown following Arukenimon's death at the hand of MaloMyotismon. It's hard to feel sorry for a villain, even if they are part of the resident Team Rocket squad, but to see his emotional meltdown and subsequent death as well makes you really feel sorry for him.
Gomamon's torture from the episode Old Reliable and his weakened state afterwards is enough to bring any Gomamon fan to tears.
The illusion TK and Cody had, as their deepest desires are impossible to ever come true. Cody just wants to be with his dad and show him the Digital World, while TK wants his family reunited. While Kari and Ken got what they wanted eventually, Cody and TK have to cope with the fact that their dream couldn't be reality (although TK's parents are on civil terms, they don't seem to want to get remarried and live together like he wants)
Wormmon's image song, "The Future You Dreamed Of, The Future I Dreamed Of."
After Wizardmon's ghost comes back, Gatomon tries to touch his hand, but they can't. So Wizardmon just floats away sadly. Then Gatomon thanks Wizardmon for the new life he allowed her to have.