Artemis stared deep into the heart of the glow cube. "But my father is so close, Butler. I can't give up now." Despite herself, Holly was touched by his unwillingness to give up, against all the odds. She was certain that, for once, Artemis wasn't trying to manipulate anybody. He was simply a boy who missed his father. Maybe her defences were down, but she felt sorry for him.
From The Arctic Incident: "Well, young man? Have you found anyone worthy of your respect?" Artemis: "Yes. Yes, I believe I have."
The Eternity Code
When Artemis finally reunites with his father, Artemis Senior.
"Arty," he cried, stretching his arms toward me. "You're a man now. A young man." I ran into his embrace, and while he held me close all plots and schemes were forgotten. I had a father again.
Juliet and Butler's reunion in The Eternity Code, after Juliet skipped out on her training with Madame Ko after finding out Butler had died for a little bit.
The exchange that occured when Juliet found out:
Juliet: You mean, Butler needs me? Madame Ko: No. I am reading the message as it's written. Domovoi needs you.
Cue Juliet running like hell for the airfield, completely abandoning her training to be with her brother.
Speaking of Butler's temporary death: "Artemis... call me... Domovoi"
A small one, but when Artemis hacks into Spiro's accounts at the end of The Eternity Code, he first intends to take the money for himself, but he remembers his father asking him if, when he gets the chance, he'll try to be a hero and make a difference, and ends up sending 90% of Spiro's billions to Amnesty International. And he makes the transaction non-reversible.
While it's somewhat subverted since he does pull a Memory Gambit, the third Artemis Fowl has one of these at the end, when his memory of fairies and all related experiences are to be wiped. He reflects on how he's become a better person and is afraid that absent these memories, he will regress to being ruthless again.
The Opal Deception
Root's Obi-Wan Moment. He isn't angry, just smiles gently and tells Holly to be well.
Artemis and Holly becoming friends again in The Opal Deception. Even though Artemis hasn't got his memories back yet, in his own words, they're "bonded by trauma".
The Lost Colony
In "The Lost Colony", there's a fleeting moment where the narrator tells us that imps never know their parents, but Number 1 used to see a female with markings like his who was looking for her son. She'd smile at him, and he'd smile back, so they could pretend to have found each other. Also something of a Tear Jerker, because it's impossible to know if she really was his mother.
In the fifth book, when Holly is killed by Abbott, and Artemis undoes her death and simultaneously defeats Abbott by shooting a laser blast into the past. However, their reactions afterward are enough to make anyone go "Aaaaaaww".
"Hey," said a familiar voice. "Don't you have a job to do, Artemis?" It was Holly. She was hog-tying Abbot with his own bootlaces. Artemis could only stare at her and smile. He still felt the pain of her death, but that would heal quickly now that she was alive again. Holly caught him smiling. "Artemis, could you get that box on to the plateau? It's a simple plan." Artemis smiled some more, then shook himself. "Yes. Of course. Put the box on the plateau."
Holly finding out what happened later, via the group's temporary mental connection as they're departing Limbo.
Artemis turned and stared at his friend with blue eyes. Holly was staring back, and she was smiling. "I remember," she said aloud. "You saved me." Artemis smiled back. "It never happened," he said.
The Time Paradox
In The Time Paradox, Artemis struggles to think of a way to make up for having tricked Holly into thinking she'd poisoned his mother with an incurable disease. He finally finds the answer when he tells Holly to contact her commanding officer while they were in the past so she could tell him everything she didn't get to say when he died.
It's made very clear that Root has a lot of respect for Holly, and was genuinely saddened by the Hamburg incident.
In the same book: whether or not you're an A/H shipper, the scene with Holly crying and smiling after healing Artemis is very touching.
"Of course I saved you. I couldn't do without you."
The Last Guardian
The dedication in the last book.
For all the Fowl fans who journeyed to the Lower Elements with me. Thank you.
When Artemis and Holly prepare to land in the solar plane. They exchange quips in the familiar way of two people who have been through much together, then Artemis looks at Holly piloting and is filled with affection for his friend, marvelling to himself how incredible she is.
Artemis looked at Holly then and felt a tremendous affection for her. He wished that he could loop the past ten seconds and study it at a less stressful time so he could properly appreciate how fierce and beautiful his best friend was. Holly never seemed so vital as when she was balancing on the fine line between life and death. Her eyes shone and her wit was sharp. Whereas others would fall apart or withdraw, Holly attacked the situation with a vigor that made her glow. She is truly magical, thought Artemis. Perhaps her qualities are more obvious to me now that I have decided to sacrifice myself.
In The Last Guardian Artemis and Holly attempting to out-gambit each other to stop the other performing a heroic sacrifice. Artemis, of course, wins. He thanks her for fixing him when he was broken, kisses her forehead, and goes to his death to protect her and his family.
Artemis: I want you to know, my dear friend, that without you, I would not be the person I am today. I was a broken boy, and you fixed me. Thank you.
When Holly passes on Artemis' kiss to Foaly.
Foaly was suddenly upset, and almost overwhelmed, but he coughed and swallowed it down for another time.
In the code down the bottom of the last book Colfer wrote Artemis's will. Half of it is, of course, jokes, until you get to:
To my friend, Captain Holly Short of the Lower Elements Police, I leave the thirty seven solid gold bars that were the price of her release all those years ago. I know that I can never make up for that crime but hopefully you can think of me as a friend when you do think of me.