The end of the chapter. Kat's boyfriend turns into a bird and flies away (forever, according to the narrator) and how does she react? "Who could cry after a week like that?"
This exchange between Annie and Renard, at the end of the chapter:
Reynardine: "Aren't you going to ask me what I did? What law I broke?" Antimony: "In your own time."
From Chapter 15: Red Returns:
The beginning of the chapter, where the normally-stoic Annie cries tears of happiness upon seeing Kat for the first time after summer holiday.
From Chapter 16: A Ghost Story:
The end is amazingly sweet. "Always remember... Remember I will never send you into danger."
From Chapter 18: S1:
Reynardine questioning Kat about Annie's life at the Court, showing that he does, in fact, care about her life.
Reynardine: "You are a good friend to her, Katerina. How is she doing in her studies? Does she have many other friends? Has anyone been giving her trouble? Has a boy caught her eye?"
From Chapter 19: Power Station:
Gamma's reappearance. After a whole chapter wandering around the dark city of Zimmy's mental landscape, they find Gamma in the only lit room, surrounded by stuffed animals. To symbolize just how much Zimmy cares for Gamma.
From Chapter 20: Coyote Stories:
Coyote juggling his eyes while reminiscing about Annie's mother, stopping when he notices it is making her sad.
"It is sad she is gone. We are all sad. All the people of the forest, and there are many."
From Chapter 21: Blinking:
Kat punching Muut (a spirit who's already established that it guides people to their deaths when their time is over) after finding out why Annie is angry at the Guides. It's such a little gesture that means such a lot.
From Chapter 24: Residential:
This touching exchange between Antimony's and Reynardine's true selves. Could they actually be... bonding?
Annie and Kat going to socialize with the other kids.
From Chapter 25: Sky Watcher And The Angel:
The end of the chapter:
Skywatcher: But there is a new statistic. The total number of angels I have seen is One.
Fans had been speculating that after The Reveal about Surma's death that someone would comfort Annie by saying something along these lines. But who'd have thought that someone would be Ysengrin?
A few strips later, we see that Reynardine would rather stay at the court with Annie rather than going back to the forest. They've bonded well, haven't they?
Tom's comment and the last two panels in the second of the link pages above also manage to be this. The little robot, who usually doesn't get such compliments, looks very happy at receiving one. And in the panel after that, the robot beside it placed its hand affectionately on its head.
From Chapter 34: Faraway Morning (And Three Short Tales):
The reencounter between John and Margo, now as an Official Couple. And, some pages later, how they got hooked up.
A subtle one, but Annie calls Ysengrin a "friend" to Jack. Considering that during their first meeting, Ysengrin tried to kill her, that's speaking volumes about their development.
Anthony has many ways to get in contact with the Court. He picked the one that would let him hear his daughter's voice.
The scenes which show that Donny may well have been Anthony's truest friend.
The ending of that chapter. "I guess this is where I'm supposed to tell you that you remind me of your mum or dad. Well, sorry, but you're your own person. I'm happy that my daughter has you as a friend."