When Marcus thinks that Koromon had forgotten him after hatching, and Koromon reveals that he remembers everything. Marcus's reaction is priceless.
On the subject of remembering, when the DATS gang had their memories erased by Kurata after returning from the Digital world in the beginning of the second half of the season, it was pretty touching when Agumon got Masaru's memories back with their little punch-out.
When Ikuto felt rejected and Falcomon told him he loves him.
Ikuto once again in the bath scene with Masaru when he asked Masaru if it's okay for him to be with everyone in the human world and Masaru replied positively.
Marcus discovering the ability to use Burst Mode. When he insists that he needs Shinegreymon's strength, his partner corrects him and says that Marcus has always been the one that's given him strength.
Their first scene together has Ikuto blushing when Chika compliments his body paint.
In the Time Skip, Keenan goes to Chika's house, so they can walk (or run) to their school together. Even more adorable when Chika grabs Ikuto's hand.
In the next to last episode when Craniamon is struggling to prevent the collision between the Human and Digital worlds, the other Royal Knights defy Drasil's orders to ignore him and help finish off the Data Squad instead helping their comrade keep the Digital world up.