In the one hour special of episode 10 and 11 Akari is brought out of her homesickness and feelings of inadequacy by Xros Heart and she and Zenjirou join hands with Taiki to DigiXros all the Digimon in Shoutmon X4 Knight. In addition, there's a subtle moment where Dorulumon is just lying down and smiling as everyone chows down on DigiNoir. Knowing his past and his attitude, this is heartwarming to see.
Episode 14 has a couple moments: when Baalmon finally accepts Taiki's friendship and calls him by his name instead of "boy" or "boy with the red Xros Loader," and Baalmon's Heroic Sacrifice to save Shoutmon X4K, leading up to his Crowning Moment of Awesome when he is reincarnated as Beelzebumon.
It's done just as well in the dub when he tricks Mikey into thinking he's recovered so he'll go and help his friends. Also counts as a Tear Jerker.
Reapmon: (grabs the Fusion Loader to stop Mikey) You don't need to worry about me any longer. Go on and join the others. They need you boy.
Mikey: But, are you sure?
Reapmon: Go! Don't lose your comrades like I did! Do as I say, Mikey.
Sparrowmon's flashback revealing that Nene isn't such a coldhearted kid after all.
Along with Sparrowmon holding Nene's hand while being intimidated by Dark Knightmon.
Mercurymon, one of the Big Bad's of Digimon Frontier makes a cameo in episode 25 as the benevolent guardian of a Code Crown and protector of his home zone. Sadly turns tearjerker because he's murdered for the code crown just after being introduced.
Shoutmon and Lunamon in episode 26.
Same episode, Beelzemon helping Shoutmon in his training, probably because he sees a lot of himself in the younger Digimon.
There's just something satisfying about seeing Cutemon finally reunite with his parents in episode 28.
When Taiki gets the last of the Code Crowns in episode 29, the zones start to merge and in a reflection of Taiki's kindness and unwavering belief that the best can be brought out in others, various Bagra Army Digimon that Xros Heart defeated are brought back to life as good Digimon. MadLeomon is brought back as a normal Leomon that the Green Zone's residents know to be a good guy and when Neptunemon is revived, Pukamon and Shakomon actually seem happy to see him. Despite his Don't You Dare Pity Me! reaction, even Grademon seems to be a changed 'mon. As if to hammer it home, the scene is set to an instrumental Triumphant Reprise of the opening theme. Makes Grademon's Heroic Sacrifice that much more of a Tear Jerker.
Akari and Zenjiro saying goodbye to Taiki before he leaves for the Digital World at the end of episode 30.
In the same episode, Taiki's speech about why he has to return to the Digital World:
“But I already know about that other world filled with life… I like those Digimon in that world who give their all in order to live. (montage of the Digimon Taiki’s befriended plays) Even though they’re monsters made up of data, they’re just like us. They’re precious friends who cry, laugh, and try their best to help us. That’s why I want another chance. I want a chance to fight and save the Digital World! I’ve already made up my mind. Besides, I can’t just leave Nene and Kiriha there…”
What's the first thing Akari does when she sees her mother? Burst into tears and hug her. It just serves as a reminder of how badly she originally wanted to go home.
Shoutmon and Ballistamon in the Gold Land arc.
To put it into perspective, Shoutmon learns Ballistamon's origins as the ultimate weapon of Olegmon. Despite this, Shoutmon never gives up on trying to save his old friend. And once he DigiFuses with DarkVolumon. He helps free the real Ballistamon inside.
Ballistamon freeing Shoutmon from Olegmon's brainwashing.
Ballistamon: You saved my life Shoutmon. Now I'm gonna do the same for you. Because you are my friend.
All the flashbacks of when Shoutmon and Ballistamon first met.
Unlike virtually every other Dark General, Olegmon is a pretty Graceful Loser.
Olegmon: (as his data disappears) Just remember this matey, friendships the greatest treasure of all. And I've done plenty of treasure huntin so I know. Ha ha ha ha!
Deckerdramon's death, also very tearjerking.
Kiriha's subsequent Character Development, leading up to him telling Gravimon that he'd rather surrender and lose than kill Taiki to win. And then Taiki jumps in front of a blast Gravimon intended for Kiriha.
The dub manages to make this even more heartwarming.
Christopher: I could never hurt you, my friend.
A less badass moment before that, but just as touching is the first time Kiriha honestly admits that he respects Taiki and also marks the first time he's openly laughed in front of the group. This amuses Shoutmon, Taiki, and Nene so much, resulting in an embarrassed, blushing Kiriha. Probably the first real warm emotions he's showed towards the team and had this troper grinning like an idiot the whole time. Shoutmon has a silly grin too on his face when he's teasing Kiriha about it.
Episode 45, Apollomon explains that he was never loyal to Bagramon. He'd only joined the Bagra Army to act as a double agent. Only wishing to protect the innocent and restore peace and justice to the Digital World. The fact that even with his plan, he still felt so guilty over the cruelty he'd inflicted on his fellow Digimon that he never healed his right arm as a kind of penance, also a Tear Jerker.
Apollomon shielding Mikey from MetalGreymon's attack, when Mikey accidentally got tossed directly in the line of fire.
In episode 46, Ewan's strategy falls apart thanks to teams Fusion Fighters and Blue Flare's Power of Friendship. A power so strong it allows the kids the power to Digi Fuse each other's Digimon. This is something that was teased before, but never shown to it's full extant, till now.
Villains or not, Lilithmon and Blastmon's sentimental moment before fusing and turning into an Eldritch Abomination.
Shoutmon doing his best to comfort Mervamon after Beelzemon's death and promising that he'll make a world where things like that can't happen, and asking her to smile.
Mervamon: You're a great guy inside a tiny body...
Dorulumon: (jokingly) He sure is... that's the only good thing about him.
The death of the true Apollomon, who thanks Taiki for defeating his evil half and tells him that it's all right if the Digimon believe that he was evil, because in the end Taiki and Shoutmon knew he believed in justice and that was more than enough for him.
Episode 50 - When Taiki decides to let DarkKnightmon send his soul to the Prison Land so that he can try to rescue Shoutmon, Dorulumon, and Ballistamon, everyone insists that they join him- starting with Kiriha!
Episode 51- Olegmon's Heel–Face Turn is completed and he joins our heroes. This manages to spark the return of the real Apollomon, who sacrifices himself so the others can return and stop Bagramon. Olegmon sacrifices himself to stop GrandGeneramon but tells the others it's all right, as he believes in them and knows they will bring him back when they win.
Oddly enough, the other seven generals themselves as well. They come to realize that Mikey was right when he told them AxeKnightmon never really trusted them. Then after their bodies are destroyed and their DigiCores are freed, they Face Death with Dignity rather than curse Mikey for defeating them again.
Episode 53 - Taiki is lost in another world after Shoutmon's apparent demise, and struggling to keep going on... when Zenjirou and Akari are able to pull him out of the darkness with a truly epic example of You Are Not Alone.
Earlier in the episode: Shoutmon telling Bagramon he'll never have what it takes to be a real king- he declares that something he learned on his journey is that a good ruler believes in his people, and even when the fail, he holds faith that they can pick themselves up and do better the next time.
Episode 54: The revival of all the good digimon that have been killed, and Mervamon leaping on top of Beelzebumon and crying Tears of Joy that he's back.
Mervamon: I'm so glad, I thought I'd never see you again.
Kiriha's reaction when he sees the revived Deckerdramon.
While it's overshadowed by the awesome factor, everyone coming in to help out the heroes and joining the Final Xros definitely qualifies. You have to look, but you can find a lot of former baddies in the group shouts, like IceDevimon or Kongoumon! It really goes to show just how good of a king Shoutmon can become, to be able to unite friend and foe alike in the final battle for their world. It also goes back to his Shut Up, Hannibal! to Bagramon, where he talks about how a true king believes in his people.
Taiki and Shoutmon's handshake before the two part ways.
Everyone helping to cheer up and encourage Yuu after all that had happened. Also, when the Darkness Loader changes colour into a yellow X Loader and the comments from the Digimemories.
Yuu's determination to wait for Damemon after he didn't show up for the Final Xros was pretty heartwarming, in this troper's opinion.