The chapter where they confront the fake pilot's parents after finding out the real reason he lied to try and prolong the divorce of the two. The remaining pilot's find his brother and tell him that his brother really was a pilot and was going to fight to protect the world even if it meant he would die. To help it sink in they prove to him that they actually pilot the Zearth and upon hearing that the boy's brother finally has faith in his family again. I can't be the only one who's heart was warmed by that.
The scene after the last battle is one too all the kids see each other once again in the afterlife and despite the problems they had with each other earlier they all come together once again and laugh and talk like children should.
In the manga, Ushiro tells to Kanji he's not in the contract right before the latter's fight. Kanji thinks that the reason Ushiro bothers sticking around despite not being involved is because of his guilt over Waku (even if he didn't actually kill him). Right before Kanji leaves at the end of his fight, Ushiro admits that Waku wasn't the only reason he stuck around for so long. Kanji pauses for a second before it hits him.
The preview for the final episode, especially when you consider that Kana will be the Sole Survivor of the kids, with her brother being chosen as the last pilot.
Kana: To my friends who fought through all the suffering... Thank you. I'll never forget any of you.
Maki makes a comment about her adoptive father watching anime while his wife is giving birth to their first child, but then he says that she is his first child. It's a shame that Maki is going to die soon.