Sindel teaming up with Jade in her route to rescue/save Kitana.
Also Sindel hugging Kitana in her ending, doubly so because Kitana had only just recovered from being mind controlled and just prior had attacked both Jade and Sindel. Especially so when you remember how, at the end of Mortal Kombat 3, it was Kitana who broke through Sindel's brainwashing and released her from Shao Kahn's control, so essentially the situation was reversed here.
In his canonical Deception ending, Bo' Rai Cho encounters the spirit of his deceased student Liu Kang. Their roles now reversed, Liu gives Cho the inspiration he needs to continue the battle against Onaga's Tarkatan hordes. Cho succeeds in beating them back and this inspires the people of Outworld to rise up against Onaga.
Ermac's ending as well, serving as the climax of his redemption arc. Being saved and showing gratitude to Kenshi in telekinesis back in Deadly Alliance is one thing. In this game, despite having fought and attempting to kill the Earthrealm warriors many times, Ermac chose to save them from Onaga's slavery. And thus, they have officially converted into the good guy status in this continuity. Even in the bleak verse of the Mortal Kombat realms, true redemption exist.