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.
"Here it is. The only thing Zimmy could ever give a damn about."
Zimmy: "I'd kill everyone in the world and then myself if she wanted it!" * 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.
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.
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."
From Chapter 38: Divine:
Zimmy shows a surprisingly tender side, though with her particular flavor of viciousness, when she agrees to help Annie and, in the process, punches Anthony Carver in the face.
Zimmy: Can't have anyone out there thinking I'm a nice person! Haha!
Gamma: I think you're nice.
Zimmy: That's all that matters to me.
A meta example. This chapter capped off a long line of stories about Annie letting her isolation and repression go and truly becoming an adult. Ever since, she's been a lot more open to everyone- instead of just Kat (and, since 'Fire Spike' the Forest-folk.)
From Chapter 39: The Great Secret:
When Ysengrin and Annie first met, he tried to kill her. How far they've come.... Which only makes it even worse later in the chapter when Ysengrin goes completely berserk and tries to kill her again. And to compound it, his first thoughts immediately afterward are horror at how he attacked Annie. Despite all of that, he really is Annie's friend.
From Chapter 40: The Stone:
This page is adorable. Even without showing any emotion whatsoever, it's clear that they really do care about each other.
Robot': But my body does not give out warmth, Shadow.
Shadow: So? It's still nice, and I can hear the thrumming in your chest when I sit like this.
Robot: It is nice.
From Chapter 42: Catalyst:
Parley inheriting the catchphrase Tom uses to refer to Eglamore after she begins training to be the next Protector of the Court. Also, Andrew and Annie just having fun in the Forest and playing around. (It's clear that Andrew is a bit rattled, but it's less genuine fear than 'OMG, what the hell is she doing?')
Also, we have Paz sending a love letter to Kat, confessing her crush after Kat thinks the letter is from Bobby... and Kat agreeing to go out with her! The look on Kat's face is just. so. sweet.
From Chapter 43: Quicksilver:
We find out that Reynard now has his own room. With shelves full of books and little ladders for him to climb on, and a dog-bed to snuggle up in! It's adorable!
This chapter also gives us this line from Reynard:
And at the end of the chapter, we find out whose house Reynardine was going to visit: Eglamore's. It says something amazingly profound about how these two have come that the mutual antipathy between them has broken up this much due to their growth and proximity to those they care about.
From Chapter 44: Crash Course:
Ysengrin is happy and laughing because Annie has proven herself to be strong.
Bonus points for the proud-father-style throw on the sixth panel of page 27. And the fact that he gets so carried away that he's gesturing all over the place.
And that he's now showing his true body around her without a second thought.
From Chapter 45: Thread:
Kat and Paz's first kiss. And then their second.
Paz: You do not have to show off for me, Kat. I am already impressed.
Renard's reaction to learning about the above, telling Kat that people are always going to fear what they don't understand, but that she shouldn't worry about what others think of her relationship with Paz.
Reynardine: As a creature in this world, you will face many hardships in your life. Who you love should not be one of them.
The revelation that Annie's disappearance isn't due to her disapproval of Kat and her same-sex relationship as Kat herself worried...it's because she realises that Kat, the most important person in her life, will leave her one day to pursue her own life, and Annie is worried that she herself will lash out in fear of this. She left to avoid doing damage to their friendship and the whole in-love-with-a-girl thing doesn't seem to have bothered her in the least.
Even softer and fluffier since Kat responds to Annie that she is the most important person in the world for her as well.