The third episode features an apparently-brainwashed Pinocchimon, and the same one Taiki and Shoutmon befriended in the previous series. When Ryouma and his group attack Pinocchimon, Taiki and Shoutmon leap to his defense, reminding him that he was their friend and snapping him out of his apparent mind control.
In the fourth episode, the student being used by Blossomon, Miho Sudo, senses the envy Yuu has toward Tagiru for having a Digimon partner while he still hasn't reunited with Damemon, and offers to destroy Tagiru to appease Yuu's feelings. Yuu refuses, saying that while it's true he was jealous of being the only one unable to help fight, he took full responsibility for Damemon's death and won't let anyone else get hurt because of it, and that he'll continue to help Taiki and Tagiru in his own way. This manages to get through to Miho, who realizes how different Yuu is from her, and enables her to break free of Blossomon's influence.
Then followed up by Tagiru assuring Yuu that he's positive Damemon will return soon, and Miho cheering Yuu on during Xros Heart's next basketball game.
Damemon and Yuu finally being reunited in episode five, at the same place where they originally met, no less. It comes with Manly Tears for both Yuu and Damemon... and more than likely, the audience as well.
The scene at the end of episode six, featuring Kotemon and Musashi's farewell, is rather touching for anyone who has a sense of the dynamic between teacher and student.
Episode nine features the return of Akari, who, despite Taiki not telling her about DigiQuartz and the new battles taking place there, reveals she'll always support Taiki no matter what situation they're in. For a girl who originally only cared about getting home, Akari's come a long way. The Ship Tease doesn't hurt either.
Nene and her father reconciling in episode ten definitely counts, especially considering what the Amano siblings went through in the previous series. Knowing that they have a father who loves them is pretty comforting.
For fans of Digimon Tamers, Takato being overjoyed at the sudden appearance of Grani.
A meta one in the final episode: Taiki passes onto Tagiru his goggles, and Daisuke yells at Tagiru to know the significance of him doing that. Even if it comes off as a bit hypocritical given how Masaru is close by - basically, this is the Digimon franchise acknowledging the importance of the goggles to being a Digimon leader.