This exchange in Final, showing Shinji and Asuka are now a real Battle Couple:
Asuka(to Shinji): "It's all right. I'll handle them. These guys aren't the real problem after all. Just take care of my cable, okay?"
Shinji(smiling weakly and nodding): "Of course."
Last word of The Final, after you find out who says it:
A good deal of "end" but especially the epilogue: in no particular order, the fact that Misato is pregnant, Aki's reaction to Gendo, the reveal that Ritsuko saved Gendo's life, Shinji admitting that he can understand his father a bit better now after almost starting Third Impact, and Gendo's thoughts just before he drifts off to sleep: "But most of all, he – for once – was as proud of him as a father could possibly be."
Asuka's comments on the final pregnancy log in chapter 6. Especially considering how frightened she was when it started.
Asuka:Hey, Baka! Thought I didn't know about your little diary? Well, I do now. You fell asleep next to it, after studying – again – until 2 o'clock in the morning. Anyway, stop worrying so damn much. I'm fine. And I'm sure – no, I know Aki is fine too. You really should stop to be so pessimistic. We have come so far, mastered so many obstacles in our lives. We will live through this as well. All three of us.
When Shinji and Asuka meet Rei III after the battle with the 16th, in chapter 9. Since Shinji is still held back by his guilt from not being able to save Rei II and his fear of having lost her forever, it's Asuka who decides to step forward and, breaking character, coaxes Rei into remembering the moments they spent together and the emotions associated with their friendship. The scene ends on a call back to the two girls' first meeting in the episode 9 of the anime.
Rei(hand held out and smiling): "It would be... convenient."
Asuka(taking Rei's hand with a grin): "Yes. Yes, it would."
Another scene between Asuka and Rei occurs earlier, in chapter 5, when they watch Shinji being rescued from Unit-01. Asuka reminds Rei of Shinji's advice to smile when she feels glad, and drops that "if [she]'d keep doing that, one could actually mistake [her] for a human being" when she does. Rei, considering her actual nature, takes it as a heartfelt compliment (which was the way Asuka intended it, knowing it would appear as a barb for any outsider) and appreciates it all the same, especially coming from Asuka.
And of course, in the last chapter, we have the grateful hug Asuka gives to an unexpecting Rei for taking care of Aki and bringing her back to Shinji and her.
Kaworu explaining that even if Shinji kills him again he'll still exist and he still loves Shinji.