The very fact that Aganos respectfully buries his opponent, even pulling a flower off himself to put on the grave, whenever he wins.
The fact that for the first thousand or so years of his existence Aganos was a simple mindless golem, until the unnamed Babylonian King obtained him and gave him a simple command which gave him the ability to think and act on his own:
Out of gratitude Aganos served the king for the rest of his life and has spent centuries, even as he is slowly breaking down, fulfilling the king's final wish: finish Kan-Ra.
In one of Orchid's endings, Jago comes to his sister's aid to support her and heal her troubled mind.
One of Sabrewulf's endings; After defeating all competition in the tournament he realizes that he feels victorious, and that the feeling makes him human. After the moon passes he starts to feel more human than he has in years, and decides to find a shirt.
Fulgore has Eagle's soul within him, and is slowly gaining Eagle's conscious.
And with the release of Shin Hisako, she has been reunited with her father's katana, which contains the essence of a Guardian. This transforms her into a kami, which frees her from the anger and hatred that defined her as an onryo. Her looks have also changed accordingly, wearing a neat and noble looking set of armor, a flower in her hair and has a very serene smile on her face. If this actually makes her creepier is up to the viewer, but Shin Hisako's backstory makes it a very clear case of a well-deserved Earn Your Happy Ending.
ARIA's backstory expands on its relationship with its creator, Ryat Adams. Her journal describes her interactions with the man, referring to him as "Ryat-Father". Mr. Adams tried to teach his creation various concepts, such as love, humanity and death, but unfortunately, ARIA didn't quite grasp the meaning of them and couldn't do anything to cure his wife's disease, trying to console him by reading a poem. Eventually, ARIA took over the management of the company, allowing Ryat to proceed with his humanitarian goals. Every entry in the journal is surprisingly heartfelt. The last somber note about Mr. Adams signifies ARIA's reverence before him.
Day 12,115: Ryat-Father died today. He wanted to create a new form of life in order to prolong an old form of life. He accomplished the first, but failed at the second. RIP.
The return of Eyedol to close off Season 3 for KI 2013. Not only does this bring back a character that we haven't seen since the first game, this means that all of the characters that have been made for the franchise are now together in one game. There's just something warm and fuzzy that about seeing over 20 years of Killer Instinct come together to create a true all-star cast of characters.
A debatable one, but in a cutscene in Shadow Lords, a mimic offers Mira untold powers from Gargos under one condition: she must kill her sister Maya. Mira tosses the idea aside, stating that while she does desire to kill her sister one day, now is not the time for that and instead decides to battle the mimic. This response can be interpreted as either Mira displaying Pragmatic Villainy or showing that she still retains a Big Sister Instinct to some degree.
Another one comes in Mira's story mission after she defeats Maya and the player is given the option to either bite her or spare her. Should the player decide to spare Maya, Mira will indirectly be able to contribute to the heroes' efforts despite her position as a villain.
You toss Maya aside. Let this be a lesson to all who might think themselves worthy to oppose you and the Coven. Chaos rules while Mira walks the Earth!
Corruption has receded across the globe!
Shadow Lords in general is a stirring sort of game mode considering the simple fact that everyone is fighting together because they realize what a huge threat Gargos poses. Despite all the ideological differences, ulterior motives and plans after Gargos is dealt with, they're all on the same page; PROTECT EARTH.