Anything with Shinji and Asuka's daughter Aki. A. NY. THING.
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 Final, after you find out who says it:
Aki: ...Mama?
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.
