The UST between Johnny Cage and Sonya. At first, Sonya is dead set against responding to any of Cage's advances, and even slaps away his hand when he offers to help her up after their spat. When he saves her from Kano, though, he offers his hand again, but pulls it back a bit after remembering what happened the first time. Sonya then smiles and willingly offers her hand, and becomes more open to him after that.
Also, Liu Kang after fighting Kitana. He acts like a perfect gentleman after the match even though she tried to kill him, and even does her the favor of acting like the fight never happened so she wouldn't get in trouble.
When Cyber Sub Zero saves the soldiers. Not only does it double as a moment of awesome for him, since he took out Goro and Kintaro in a tag match, and devastated Ermac immediately after that. In the cutscene that follows, the soldiers surround him and shower him in praise, thanks, and admiration. It's doubly effective since Subby just admitted to feeling rather guilty at all the horrible deeds he did while Brainwashed and Crazy, so it's nice to see his good nature shine through and rewarded in such an effective way.
Speaking of which, in the intro for his chapter, what is the first thing he sees upon having his free will restored? His friend, Smoke.
Kratos' Arcade Ladder Ending, probably the first time a God has showed him any form of respect or did not backstab him in the end. The narration stresses how surprised and unused to this the Spartan is.