Athrun's open sorrow when The Freedom is destroyed, and Kira is presumed dead.
And some could argue that when Shinn comments he did it for Athrun could count. Though it only threw salt into the injury for Athrun.
Phase 43, Neo to Murrue:
"I think that maybe... I know you. Yes... I know you. My body knows. My eyes, my ears, my arms... And that's why I couldn't just fly off. I think I know how hard it's been for you. It's been hard for me too. I would like... to stay right here, with you, by your side."
"Don't worry; I'll never leave you again... Murrue."HE'S BA-ACK!!! What lead up to this was quite possibly the biggest CMOA in the entire Gundam franchise, and this just seals the deal.
You know what? Shinn and Kira meeting face to face and becoming friends at the end of the Special Edition. Take that Hatedom—everybody wins.
Rau's interactions with Rey in the flashbacks. Durandal's father/son moments with Rey could also count.