Rebuild of Evangelion/Heartwarming

Shinji getting Rei to smile in the last few minutes of the first film.
Their hug at the climax of the second movie is definitely one, too... even if it means the world is ending is the result.
- There's also the beginning of Shinji's whole Eva restart sequence.

Shinji: I don't care about the world... I don't care about anything. I. Want. Ayanami. GIVE HER BACK!

- Not to mention that Giant Red Rei smiles as she merges with Unit 01.
Rebuild of Evangelion 2.0's ending has Shinji declaring that to him, Rei's life worth MUCH more than the world. Then he proceeds and kicks MASSIVE amounts of ass. The movie ends with Shinji and Rei embracing inside Unit 01's entry plug as Kaworu is approaching in the Mark.06 to prevent Third Impact from succeeding ahead of time. Made even better by the fact that earlier in the movie, Asuka sort-of confirmed that Rei reciprocates Shinji's feelings even though she doesn't know it yet.
- It's a testament to the strength of the scene that you don't care that Shinji has effectively brought about The End of the World as We Know It, because after everything he's gone through, he finally had a triumph.

Rei: "It's alright, Ikari-kun. If I die, I can be replaced."
Shinji: "No! You're the only you that exists! That's why I'll definitely save you!"

- Speaking of Asuka, she had gone somewhat Out of Character by volunteering to test Unit 03 so that Rei can spend time with Shinji, getting almost killed as a result. And that smile on Asuka's face when Rei thanks her via voicemail... keep in mind: Rei never thanks anyone except Shinji and Asuka, not even Gendo.
  - In the series, Rei was just ready to blow up herself because she considers herself to be worthless. This time, she does it so Shinji never has to get into an Evangelion ever again. Yep, he left her to basically mope in a corner, and she's still willing to die for him.
- Asuka's confession to Misato that although she doesn't want to depend on others, she actually likes the feeling of being nice for a change.
  - Sadly in true Evangelion fashion it's all stripped away in the matter of seconds.
Gendo, of all people, deciding to Pet the Dog and actually go along with Rei's plan to hold a dinner party for everyone, after seeing Yui's face reflected in Rei's. Sure, he goes back to being a total bastard sometime afterwards, but for a fleeting moment, he was content with doing something good.
The moment when Asuka sees the bandages on Rei's hand and then looks at the ones on her own hand. What was about to degenerate into a fight becomes a Not So Different moment.
There is something just adorable about hearing Rei try to describe her feelings.

Rei: When I'm with Ikari, I feel warm and content. I want Ikari to feel warm and content too.

In 2.22 the moment when Asuka smiles sincerely after a conversation with Misato.
More than ten years after she was first mentioned, we FINALLY get to see Toji's little sister. And she's all better!