In X's ending for Megaman X4, X asks Zero to terminate him if he ever goes Maverick. Zero's response? "Don't be absurd." The unspoken message there is that Zero doesn't think that X could ever be corrupted by the Maverick Virus.
Zero's return in Megaman X6. The music, and the joy in X's voice when Zero reveals himself really sell the moment.
In Megaman X6's Good Ending for X, he brings back a mortally-wounded Gate for Alia to try and repair, as she used to be his best friend. Really, that whole ending is pretty heartwarming—the rest of the Maverick Hunter team shows up to offer their support in restoring all the damage caused by Sigma's Colony Drop in Megaman X5, leading to the most optimistic ending in the series.
In Zero's X6 ending, when he's sealing himself away to purge the Maverick Virus from his system completely, the scientist in charge of the operation is concerned about what might happen in his absence. Zero calmly replies not to worry about it, as X will always be there to protect the world. He's got that much faith in his partner.
X finally warming up to Axel by the time of Mega Man X8.
Dr. Light hugging Mega in the Bad Future episode. Mega Man had been gone for about 30 years due to a time travel mishap, and the city had been taken over by Dr. Wily. Having found that Roll and Dr. Light were imprisoned, he broke in to break them out. Light, who had been scribbling equations on the cell walls, turns at the sound of his voice.
Dr. Light:Mega! [hugs him]
It even gets a callback when they hug again at the episode's conclusion after Mega returns to the present.
Mega hugging Roll at the end of "The Incredible Shrinking Mega Man."
Roll hugging Mega Man at the end of "The Strange Island of Dr. Wily."
Any time Rush goes jet mode by himself to save Mega.
Dr. Light's fatherly love for his creations is present in virtually every adaptation of the series, but the comics bring just how much his Robot Masters mean to him to the forefront, especially Rock, Roll and Blues.
Dr. Light: I constructed two advanced A.I. robots. You would call them models DLN-001 and DLN-002, but I call them my children. I may have built them by hand, typed their coding myself, but as my children...they have enriched my life and helped me grow as a person.
When Mega Man suffers a breakdown from destroying the reprogrammed Light Robot Masters and scares Roll off with his actions, Light holds him close and convinces him he isn't "evil". Later, when Rock wakes up from Ra Moon's EMP, the first thing Light does is scoop him up and comfort him.
After seeing Roll's heroics on television following the shipwreck, he rushes to the site and gives her a So Proud of You embrace.
The entire flashback to Blues' upbringing and running away, while simultaneously a Tear Jerker, counts, from Light welcoming his first son into the world with a joyous hug, to the montage of him teaching Blues of the world, including sharing a night at a concert, showing him around an art museum and buying him his trademark scarf.
One sweet moment, after the EMP field hit, Break Man checked on his offline brother and injured sister. And then what he says, is an attempt to apologize to both.
The segment in Blues' backstory where Dr. Wily drops by to cheer up Dr. Light after Blues runs away. Their relationship may have fallen apart later on, but it really comes through that they used to be good friends as well as colleagues.