And, by extension, When Tomoya and Nagisa forget Fuuko for half a day, then remember when prompted by Koumura-sensei. Nagisa shouts out "Fuuko-chan!" and they both turn to see her standing behind them. She had been following them the entire half-day, confident that they'd remember her.
Kotomi receiving the teddy bear her parents sent. The entire arc is pretty much made of heartwarming, with all of the other main characters befriending her and coming together to help her just when she really needs it.
Clannad is absolutely packed with these, but episode 18 of ~After Story~ takes the cake and eats it too- the scene where Tomoya's estranged daughter Ushio tells him that she has to find the robot he bought for her rather than getting a new one when she lost it because it's her first present from her Papa, and Tomoya tearfully embraces her while promising to be a better father to her reduced me to tears. Followed by Tomoya himself crying openly on the train while telling Ushio about how he met Nagisa. Watch it here.
Made insanely Tear Jerker level by the Crowning Music of Awesome with Negai wo Kanau Bashou (The Place Where Wishes Come True)'s second version, with the whole orchestra coming in just as Ushio starts crying in Tomoya's arms. And it just continues on as Tomoya recalls Nagisa and finally allows himself to cry over all the good memories.
Tomoya: Nagisa, I finally found it. The thing only I can protect. It was... right here.
Episode 19 of ~After Story~ had a couple major ones. In the beginning of the episode, Tomoya spends the day with Akio and Sanae, after finally snapping out of his five-year Heroic BSOD. Akio, during a game of baseball, says it best
Akio: Welcome back to the world of the living, kid.
And then there's the moment when Tomoya finally reconciles with his father.
There's minor one during the basketball game in season 1. The Basketball Club captain and the other upperclassmen were willing to risk their club supervisor's anger because they wanted to see such a talented player like Tomoya play again, and after Tomoya, Sunohara, and Kyou win, the team captain even compliments Tomoya. They provide a great contrast to the soccer club, who enjoy tormenting Sunohara.
The entire middle section of episode 22 of ~After Story~, a montage of the reset button ending that covers where all the characters are now,consists of the biggest ongoing Crowning Moment of Heartwarming in the history of human fiction. It's a Crowning Half-Episode Of Heartwarming. Mere words cannot describe it, but it reduced me to tears AGAIN- tears of pure joy. Especially as up to that point it looked like the series might be going out on the bleakest of Tear JerkerShoot the DogDowner Endings.
Nagisa: As long as we've been together, I've known you were the only one. And even...
Tomoya: Even if I'm like this? Even though I'm so pathetic...
Nagisa: It's fine, I'm pathetic too. But, I think if we're together, we can grow stronger.
Tomoya chokes up in tears and hugs her
Tomoya: Will you stay with me?
Nagisa: Yes. Of course I'll stay with you. No matter what happens. For as long as we live.
The baseball scene in Episode 20 of Season 1 (21:25) when Nagisa accidentally confesses her love of Tomoya is just adorable.
The end of Kotomi's arc in season one. After having spent all the years since her parents' death thinking they had loved work more than her and trying to repent for burning what may have been the last remaining copy of their potentially world-changing research, her parents' colleagues deliver something that her parents must have spent their last minutes trying to save just before their plane crashed, abandoning their research so that it could fit in the suitcase: a teddy bear, the birthday present Kotomi had asked her, along with a note written in English leading that whoever finds the bear deliver it to their daughter. Then comes a montage of the note being read in dozens of languages and the suitcase being passed from hand to hand, until it finally reaches the people who will be able to safely deliver it...
I could hardly contain the feelings of pure heartwarming in the last episode of Season 1. When Akio came skidding into the packed school auditorium to deliver one of the greatest of all possible Get A Holdof Yourself Man speeches to a crying Nagisa at the top of his lungs, affirmed by Sanae and Tomoya. "We let our dreams become your dreams! Because that's what parents DO! That's what family does!" So amazing it should also be Crowning Moment of Awesome.
I can't believe no one has mentioned the moment at the end of this episode when Tomoya finally gathers up the courage to tell Nagisa that he loves her. Nagisa's subsequent reaction, combined with the Crowning Musicof Awesome in the background led me to fight back tears of joy. This could also count as a Crowning Moment of Awesome.
After Story episode 19. Tomoya finally tells Naoyuki that his efforts to raise a child alone were not in vain and he finally gets some rest.
After Story episode 20 when Fuko visits Tomoya and Ushio and ask's what was her mother like.
Fuko (To Ushio): You've never met your mother, right?
Tomoya: No. She only knows her face from pictures.
Misae's arc in After Story always leaves this troper's heart full without fail even during the sad moments.
The entire latter part of Fuko's storyline in the Visual Novel, particularly the end, where she's finally able to wish her elder sister congratulations and happiness in marriage before her ghost disappears completely.
Her True Ending in particular is simple, but heartwarming, suggesting that she has woken up from her coma:
Fuko: If you don't mind, please go out with Fuko!
The end of season one's last official episode, episode 22.
The second half of ~After Story~ Episode 18, where Tomoya, after finding out his dad's motives for winding up the way he is, realizes he became just like him. The kicker starts when he goes back to Ushio and reconciles with the estranged daughter who he never once really LOOKED at for five years after Nagisa's death, and both of them erupt into tears. He thereafter takes her in as his own.
In ~After Story~ episode 19, when Tomoya finally reconciles with his father.
The ending to Yosuke Yoshino's backstory. After the crash from stardom, Yoshino returns home. And who's there at the bus stop waiting for him? Fuko's sister, Kouko, who welcomes him back with open arms as he embraces her.
Episode 8. Sunohara has gone to the hospital and seen Fuko. Next morning, he can't remember why he was even there and of course can't remember Fuko. But then he starts vaguely remembering her, even stating that he doesn't think he hated her. What he said about himself was true. Deep down in his heart, he is a good guy.
It's a subtle thing, but in the recap episode, it's made clear that Ushio calls Sunohara 'Uncle Youhei.'
Also, Tomoya mentioning that everyone reunited to celebrate New Year's Day.
To be precise, this moment comes in episode 22 when Tomoya suddenly returns back to the foot of the hill where he met Nagisa, watching her walk away after he decided that they shouldn't have met when she died. Realizing where he is, Tomoya calls out her name and starts running to her, embracing Nagisa as the colors of the setting turn vibrant again. Their conversation right afterwards is also very sweet.
Nagisa: I'm glad that I met you. I had a wonderful life.
Nagisa: So please, don't lose yourself. No matter what may await, please don't regret meeting me.
Tomoya mending Ushio's turtle toy when spending a day with her after being estranged from his daughter.
The ~After Story~ OVA "The Events From One Year Before", where Tomoya and Youhei's prank leads to Nagisa making a friend.
Tomoya remembering his first meeting with Youhei (orchestrated by Koumara-sensei) after both of them had been in fights. They saw each other's bandaged faces and laughed.