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?
The flashback with Surma and Anja talking about their friendship in pages 436 and 437. Bonus points because their respective daughters would mirror this same moment almost forty chapters later.
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.)
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.
Every time the headmaster tries to shut Antimony down, someone steps up and has her back. Even more satisfying than seeing the Court's red tape come back to bite them in the ass.
When the court chooses Smitty instead of her as medium and tries to bar her from visiting the forest, Coyote immediately offers to make her his medium instead.
When the headmaster tells Jones to advise "your student" against taking Coyote's offer, Jones bluntly points out that since he ended Antimony's candidacy for the medium position, she is no longer Jones' student.
Finally, when he threatens to cut off all support from the court, Smitty quickly steps up in his new capacity as medium and offers Annie his support on the court's behalf.
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 and the fact that he gets so carried away that he's gesturing all over the place.
Ysengrin: Hahaha! Beautiful! You looked beautiful!
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.
When Kat asks Annie why she came to the tree room but didn't enter, Annie replies that it's where she realized she made her first friend, and that she couldn't enter until all was well between them. They decide to enter together, and walk toward the tree holding hands.
From Chapter 47: See Ya!:
The bonus page. Wait for it: Boo!
Chapter 48: Tall Tales:
The fairy and rabbit's relief and joy that they'll be able to see each other even after the rabbit has gone to the Court.
From Chapter 51: The Tree:
The relationship between Antimony and her classmates have clearly changed over the years. In the early chapters, Annie was a complete loner before meeting Kat. By this point, most of the students look shocked and enraged when Anthony humiliates his daughter in front of the class.
Despite Kat being justifiably hurt and angry over Annie constantly stealing/copying her homework - without permission - she still leaps to her defense when she hears Anthony Carver wants her to repeat Year 9.
Antimony returns this. The one thing she fears the most is being separated from Kat, yet even as rattled by her father as she is, she desperately and loudly exonerates Kat from any blame before Kat can potentially say anything stupid in righteous anger, despite knowing it's going to mean her worst fear realized. Moreover, the normally self-assured and stubborn Annie is completely cowed by her domineering father and won't even speak up in her own defence... but just let him even vaguely threaten Kat and Annie goes flying to her aid.
The little forehead touch between Kat and Annie after Kat gives her the walkie is precious and heartbreaking at the same time. They don't even know when Annie's new restrictions will let them see each other, but Kat wants to give her every comfort she can.
Annie's classmates all came to see her off. Relationship evolution indeed.
From Chapter 52: Sneak
The boys in Annie's year make her a card after her father tells her she has to repeat the year. "Sorry about your hair and your Dad" aside, it's heartwarming to see how much Annie's relationship with her classmates has evolved.
This page implying that Annie didn't pass complete control of Reynardine to her father. Despite all the tearjerkers that have come from the last chapter, some of Annie's fighting spirit remains when it comes to her friends.
When Parley and Andrew Smith come to visit, they say to Annie that Coyote is unhappy about turn of events. Moreover, several denizens of forest mention that Ysengrin is sure that Annie is held against her will. It is heartwarming to see how much friends Annie has in both Court and Forest, as well fact that Coyote is taking this seriously and is angry that she's been barred from the forest. And later, Kat, Parley and Andrew go together to search for Reynard
When Kat, Parley and Andrew find Rey in Anthony's house, the very first thing Rey does is worriedly ask after Annie. Keep in mind, this is after she handed him over to Anthony (after transferring control of him to Kat). As one commenter put it: "Might not have become Surma's lover, but heck if he ain't gonna be a better dad than the guy who did."
Donny once told Annie that Anthony could only ever drop his guard around a select few of his friends. In the present day, it still holds true. Donny goes to see Anthony alone, and for the first time since his return, Anthony Carver is relaxed and friendly, even cracking a joke. It's clear that Anthony still considers Donny a friend, despite everything that's happened.
For an added bonus, Annie is watching them from the blinker stone in Donny's pocket. It's probably the first time in her life she's seen her father like this.
The real reason for the past few chapters. The Court was going to kick Annie out for her activities with the Forest, so Anthony made a deal to protect Annie by having her fall into line with what the Court wanted. He was protecting the only other person he loves. Bonus points for him feeling remorse for what he's put her through.
In chapter 54 Coyote calls a meeting with the Court. Why? Because he hasn't seen Annie in a while and he misses her.
It becomes clear after several pages that Coyote, in his own self serving, sociopathic way, cares a great deal about Antimony and wants her to be happy.
According to Coyote, he could eat Anthony and no one would care, except for Annie. So he won't.
Antimony's smile in the last panel. After all the crap she's gone through in the last few chapters, she seems to have regained just a spark of self-confidence.
Ysengrin shows his affection and concern for Annie in his own way: he shatters her blinker stone and forces her to face her rage, even if it means she'll turn that fire on him, because that is who she is and he will not let her diminish herself.
Even caught off-guard and at the mercy of her own suppressed rage, Annie is horrified at the thought of injuring the (formerly-a-rabbit/jackalope) student that she has been assigned to protect, to the point that his approach stops Annie's fury in its tracks. She manages to get a handle on her fire powers quickly enough to avoid disaster.
As for the student? They're relieved to recognise the forest medium (they couldn't identify her without her fire-self), and is completely undaunted by the pyrotechnics — in fact, the fire-fest reassures them that Annie is a friend. Rather than fleeing, they switches from hanging back shyly to delightedly calling out to her and then leading her away, chattering happily. They're also on a first-name basis with Andrew, suggesting that Smitty's doing a great job in his role as Court Medium.
Despite the inevitable damage that occurs when fire meets wood, Ysengrin is unperturbed by the incineration of his arm. Apparently, sorting out Annie's psyche was far more important. Even if he is able to regrow limbs, it says much about Ysengrin's priorities.
Rabbit kid is finally reunited with their fairy friend. They embrace as well as a human child and tiny fairy can, and it's as cute as one would expect.
In Chapter 56, Robot shows Shadow the new touch-sensitive arm Kat installed on him. The first thing Shadow does is pet and cuddle it, proving that Robot is capable of blushing.
Shadow: Hey, you got your new arm! Lemme see! *notices Robot's bandaged finger* Shadow: What's this? Robot: I broke my finger. Shadow: *distraught* Whaaa?! Robot: Do not worry, it does not hurt now you are here.
Robot becomes flustered and changes the subject. Shadow responds by reaching out and shyly holding Robot's hand, indicating that Robot's long-held crush on Shadow is officially reciprocated.
In Chapter 57, Reynard is helping Annie re-establish her powers after Ysengrin's destruction of her blinker stone...and providing a friendly ear as Annie cautiously begins to reclaim her emotions. He's supportive and comforting, acknowledging that her anger is a problem and that she's having trouble without the blinker stone, but reassuring her that these problems are only temporary and she'll soon be back to normal, if not better — as long as she can deal with her emotions instead of cutting herself away from them. This results in Annie bursting into tears, desperately apologising to Reynard for surrendering him because Anthony told her to. Reynard's response is to snuggle under her chin and tell her that she doesn't need to concern herself with that just now. After so many tough lessons for Annie, it's nice to see Rey taking the "spoonful of sugar" approach while still helping Annie learn what she needs to, and offering fox-cuddles in the process.
Though Winsbury's confession was forced, some of the sentiments behind it — his respect for Annie and how everyone misses her — are genuine, as he and Janet later affirm.
Janet: You see I know he respects you greatly, Annie. And the fool that I am, I teased William about you! ...
William: You know, despite everything, I was being honest before. We do all really miss you. You're our friend, and we hated seeing you go.
Annie: You don't need to worry about me so much, Kat. I couldn't ask for a better friend. I'm getting myself back together. And right now this is all I need. [touches Kat's hand on her arm] This, right here.
In chapter 58, <snuffle> and her formerly-rabbit friend spend the day together and have a gushy goodbye.
Jeanne being reunited with her lover after centuries of being forced to serve as the sentinel of the Annan river.
Freed from being a "psycho rage ghost of hate", one of the first things she does is to remove the gash she'd left on Annie's face with her sword, with a single swipe of her thumb.
In the course of Parley's swordfight with Jeanne, Smitty is stabbed with Jeanne's dagger and badly injured. Parley freaks out and asks why his powers didn't keep him safe. Smitty tells her that his powers worked fine - the knife was meant for her.
The absolute loyalty Kat shows when she argues against Red's condemnation of Annie. She points out that all of the individuals involved chose to be there, no one of them could have done anything on their own, Annie pulled together a plan that gave them a solid chance to succeed, and that everyone involved (save Ayilu and Red) knew Annie very well and trusted her to do the right thing. In spite of everything that's happened up to this point, the friendship between Annie and Kat is still rock-solid.