When Dexter learns that pirates kidnapped his sister in "Ocean Commotion" (they believed she was a mermaid due to her swimsuit), he goes straight to the pirate ship and reveals his Giant Mecha, which he had intended to keep secret, to save his sister, even though it would be easier for him if she were out of the picture.
In a weird way, the ending to "Beard to Be Feared", even though it's had some Memetic Mutation:
Action Hank: "It doesn't matter if you have the beard on the outside, as long as you got the beard on the inside."
"Way of the Dee Dee" has a lot of these moments, mostly involving the times in which Dee Dee tries to teach Dexter how to have fun/how to act like a playful kid. And even the ending, where, for once, Dee Dee is genuinely apologetic for the chaos she (albeit unintentionally) induced.
In "Dee Dee Locks and the Ness Monster," Dexter's mom asks Dexter to read to a sick Dee Dee, who's genuinely touched by the gesture. As Dexter begins to read to her, Dee Dee, smiling weakly, cuddles up to him and folds her arms over his head. A sweet image.
In the episode "Dee Dee's Rival" you can see the difference in the way Dee Dee and Olga (Mandark's sister) interact with their brothers. Both of them want something from their brothers, but Olga threatens Mandark (he begs her not to hurt him) and at the end of their conversation, flicks his nose in a way that looks painful. Dee Dee, on the other hand, pleads with Dexter and when he agrees, kisses him on the nose making him smile.
Monkey getting Simian to do a HeelFace Turn by offering him a banana.
Koosalagoopagoop finally being accepted in The Land of Koos. The Tastes Like Diabetes atmosphere only added to the cuteness.
Most of the episode "Snowdown" is about Dexter's dad teaching him how to snowball fight to defeat Dee Dee who's pelting him with snowballs. When he finally does manage to score a hit on her, however, she sincerely congratulates him on it, earning a sincere thanks from Dexter. Despite Dad's melodrama, Dee Dee ultimately just wanted to play in the snow with her brother, and Dexter was fine with that once he figured out how.
"Nobody bonks my sister but me!" Nothing annoys Dexter in the world more than Dee Dee, but messing with her will set off his Berserk Button in a way that messing with his lab has never accomplished.
The ending of "Sun, Surf, and Science" where Mandark befriends the surfer dude.
Also, him trying to save Dee Dee.
The entire episode "Glove at First Sight" is pretty sweet, since it tells how Dexter's parents first met. Not only is the slobby Dad shown to respect Mom's obsession with cleanliness and help her try and overcome her germophobia, but it's also revealed that Mom's trademark latex gloves were in fact a gift from Dad.
In the quiz in episode 20 the final question is to identify each others favourite thing in the world. Dexter's is his lab but Dee Dee's favourite thing? Dexter.
Dexter's and his family pulling together to defeat the Kaiju monster in the episode "Last But Not Beast" was surprisingly touching.
Dee Dee meeting Sasquatch in "Sassy Come Home" and the two becoming fast friends.
The entire graphic novel "Dee's Day," written by Derek Fridolfs, is this. The plot is essentially a play on the "It's a Wonderful Life" trope, in which Dexter wishes Dee Dee out of existence. At first he's content with this, but then begins to grow bored with his life... and then remorsefully tries to find his sister in a parallel dimension because he misses her. He does eventually find her, but she exists in a dimension where she doesn't know him, and he desperately tries to convince her to come home. Eventually she does, and the comic ends with the two of them genuinely bonding with each other, with Dee Dee teaching him how to dance.
Another example from the comics, (specifically, the Cartoon Network crossover ones.) Dexter accidentally turns himself into a cat. Dee Dee is absolutely thrilled to find a cat to play with, but Dexter eventually turns himself back into a human. Dee Dee, having no idea what happened to her new "pet," is in tears, convinced that the cat ran away. Dexter, feeling genuinely sorry for his sister, makes her a robotic pet cat to play with, and the comic ends with both of them happy.
The end of "Accent U Hate." The next day after a group of kids with "funny accents" stand up to the bully who was going to beat up Dexter and his friends because of their accents, they run into him. He turns to them and Dexter and his friends shiver...right up until he turns around, revealing he's wearing a new shirt that says, "I Love Kids With Funny Accents."
The Justice Friends episode "Krunk's Date". Not only is it clear that Krunk and She-Thing love each other, but Major Glory and Val Hallen are both shown to be supportive of the relationship and even comfort Krunk over She-Thing going to jail.
In the episode "Poppa Wheeley", Dexter creates a fake scientist dad for Career Day because he's worried that his classmates would find his real dad uncool. While his real father is initially upset that his son doesn't think he's cool, he does come to the rescue when everyone boos Dexter's fake dad and impresses the entire class by doing several biking stunts. Dexter reconciles with his father and even gives his fake scientist father the boot.
Dexter's elation at seeing his sister again in "Oh, Brother", especially since turning his sister into a brother had the unforeseen side effect of the boy genius becoming The Un-Favourite to his family.
In its own weird way, Dee Dee dyeing Dexter's hair blonde in "The Blonde Leading the Blonde" as well as Dexter thanking Dee Dee for her actions. While Dee Dee mainly did it to prove the belief that blondes have more fun, it's nice that she chose to prove the theory in a way that allowed her brother to have a nice day and that Dexter was grateful for his sister's selfless decision.
A small one, but one brief scene in "Poetic Justice" shows Dexter and Dee Dee sharing a single scoop of ice cream.
"Coupon For Craziness": The ending where Dexter reunites with his family and joins them in the coupon ritual he had initially scoffed at, having learned to appreciate them after having to spend a day with scientist parents with no love.
"Bygone Errors": The elderly Dexter and Dee Dee sit around talking about their Glory Days. At the end, Dexter falls asleep in his rocking chair, then Dee Dee puts a blanket around him and leaves the room.