Robert's interactions with Tron, especially when his memories of her return.
Robert saving Bass when he's about to overload.
Tiesel and Denise's date, which ends with them becoming a couple.
Denise Marmalade's family and friends helping her through her problems.
The tail end of Arc 3 has Dr. Light admitting he was wrong and promising to make things up with Robert; Robert does likewise and lets go of his hatred as well.
The Arc 3 finale has Robert's conversation with his deceased father, Anthony Light. It also has Robert, Dr. Light, and Tron decisively making up and looking towards a better future.
Roll's reconciliation with Robert and Tron at the end of Arc 4, chapter 1.
Rush and Bon playing together in Arc 4.
Arc 4, chapter 2, has all the scientists at the robotics convention volunteering to fix Rush.
Tron and everyone else planning Robert's birthday party in Arc 4, Chapter 3, and the party itself. Even more heartwarming is the presents they give him, including his father's journal, a new battle chip system, comics and manga, and a Servbot of his own.
In Arc 4, chapter 3, Robert talks down a man from committing suicide.
Protoman giving Robert a birthday present at the very end of Arc 4, chapter 3.
Glyde paying for Wily's bail is a villainous example.
Arc 5, chapter 1 has Roll helping Robert against Magnet Man, and vowing to help him however she can. Robert is proud of her, and allows her to fight in his stead while he's being repaired.
Tron helping Roll out after her fight with Break Man in Arc 5, chapter 2.
Dr. Light giving everyone a day off from work due to their stress.
Bass secretly helping Roll against Hard Man.
Robert getting angry when Snake Man attacks Rush.
Break Man saving Robert from Snake Man's poison.
Mega Man and Rush working together in Snake Man and Gemini Man's chapters.
Robert telling Doc the Met about his encounter with Snake Man as a bedtime story.
The bond between Gemini Man's two personalities is touching, especially when one tries to save the other from dying—and when it fails and he's defeated too, he's happy to see his 'brother' again.
Robert and his family and friends, as well as Tron's family, supporting her when they learn she's pregnant.
Tiesel deciding to take on two Doc Robots solo because the Servbots aren't made for warfare.
Tron and Tiesel added a Mega Buster-like gun to the Gustaff in honor of Robert.
Robert and Roll save Break Man from a vengeful Bass. In return, he tells Robert his real name, Proto Man, and gives him the truth about what's been going on.
Robert talks with Dr. Light about his anger reemerging and receives support and advice on it.
For the three year anniversary, the writer thanked the readers for supporting the story for so long.