Magneto's ending, where he uses Galactus's vessel as a new home for all the mutants on Earth. It's helped by the music being somewhat melancholic, as he finally fulfills his lifelong dream. And if you have doubts, remember: Magneto never was a true villain, but rather a Well-Intentioned Extremist.
Hsien-Ko's ending. Hsien-Ko and Mei-Ling go to meet Doctor Strange so that he can put their mother's soul to rest and return them back to normal humans. He does so without any reluctance... And then the dialogue reveals that the ending isn't real, but is a comic book the sisters drew together to deal with their troubles. Despite all this, they're still happy with life (Or rather, undeath).
In Ultimate, they actually meet the the good doctor — who is concerned about them and wants to help.
Storm's ending. She has doubt over the humans on Earth that she saved because they still have discrimination towards mutants like her. But Black Panther, her husband, says that she did the right thing and as long as he has the land of Wakanda as well as Storm besides him, he could fight any threats that ever come to his land. She then says that it's their love that gives her hope and that hope will see her through difficult times.
Super-Skrull's ending, where he turns the Skrull Empire into a force of good for the universe, protecting it against another threat like Galactus. The Skrulls are now heroes, and everyone everywhere lives a life of safety and prosperity thanks to them. Even if he is just using the power for his own use.
Any time Felicia interacts with Amaterasu. Awwwwwww!
For that matter, Amaterasu licking Morrigan's face in the opening cinematic.
against Chris: Rarely have I met a man with such a strong moral compass. My sole regret is that we had to meet in combat.
against Phoenix: I hated to do that to you, Jean. You are like a sister to me.
Hawkeye's win quote against Captain America.
I may give you a hard time, but the truth is, there's nobody I respect more than you, Cap.
One that sticks out is the fourth opening that serves as a Book Ends. With Ryu reaching up for someone's hand, at first it showed that there was no one really there, and he had to pick himself up again for another brutal showdown. But the second time? The man who faced him in that show down took that hand and is smiling, ready to bring Ryu back into the fight against their allied foes.
The Hulk's ending. Especially if you ever played Resident Evil 3. He and Chris beat the ever-loving crap out of Nemesis for all the trouble it caused Jill. It's both hilarious, awesome, and heartwarming rolled into one package.
A small one, but when playing on the Kattelox Island stage, you might notice Teisel Bonne standing there. He never reacts to what's going on unless his sister, Tron Bonne, is fighting. The second she leaps into the fray, he starts cheering her on and celebrates if she wins.
Thor's quotes when fighting Amaterasu show nothing but the purest respect.
(Battle starts) 'Tis fitting that two gods meet in battle thusly!
(Win-screen quote) Thou art a most courageous god. The inhabitants of Nippon are truly blessed to have you as a protector!
A bit of fridge heartwarming, in one of the trailers, Chris is seen catching a falling Morrigan after she's shot down from the sky. Keep in mind, Morrigan comes from a universe where her mere existence is enough for people to want her dead, so a human saving her must really mean something to her.