Cagalli receiving the Akatsuki, along with a recording from Uzumi, encouraging her to trust in her friends and loved ones. She then takes off to defend her homeland.
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.
At the end of the special edition we're treated to a scene of Kira and Lucas running up and embracing each other when they cross paths in one of the PLANTs. About half those present watch the two with warm, amused smiles, while a number of others go a bit slack-jawed, including Shinn and Luna. Manages to be funny and heartwarming at the same time.
Shinn's expression is rather noteworthy because he comes across as a lot more... relaxed than any other time in the series. Maybe he's finally found a bit of peace.