Sofia and Amber connecting as real friends and sisters at the end of the pilot movie.
Sofia: You have no idea how happy I was when I found out we were going to be stepsisters!
Amber: Sofia... we're sisters.
A subtle example, but in "Just One of the Princes", there's a bait-and-switch moment where Sofia thinks she's getting a majestic black pegasus to ride, but her horse actually turns out to be a small purple Pegasus with small wings named Minimus. Sofia still reacts with joy, and even when Minimus advises Sofia to switch horses (and more than once at that), Sofia adamantly insists that she can win the race with Minimus. And she's right, she does tie for first place with James.
Baileywick having tea with Sofia after she's grounded for bailing James out of trouble.
The ending of "Cedric's Apprentice": Cedric has the chance to use his invisibility potion to steal Sofia's amulet, but because she helped him prove what a good sorcerer he is, he decides against it.
Not to mention the episode's epilogue. Heck, almost all of Cedric and Sofia's interactions in that episode could count.
When Sofia first turns herself into a lizard by accident, Cedric doesn't even think for a second of using the opportunity to steal the Amulet from her, instead reassuring her that she'll be fine before casting the spell to return her to normal. Knowing that he could do it is exactly why she pulled off her Batman Gambit later.
Sofia and Clover reconciling in "Blue Ribbon Bunny."
In "The Princess Test", Amber encouraging Hildegarde to keep going in the test after Hildegarde had given up.
And Sofia passing the secret "kindness" test by agreeing to help Mrs. Higgins, and then insisting on continuing to help her even after running into obstacles (even after Mrs. Higgins tries to reassure Sofia into going back for the princess test).
In "Baileywick's Day Off", four simple words at the end after everything that happened: "Baileywick is more important."
Amber and Sofia ending up having a good time together in "Two To Tangu."
The ending of "A Little Witch". Predictable, yes, but heartwarming? Definitely.
In "Princess Butterfly", Amber is about to pull a Karma Houdini: after an episode of trying to take Sofia's amulet, Sofia finally just offers the amulet so Amber can fix her magical butterfly costume without having to admit to the fairies she cheated to win the earlier costume contest. After all, to Sofia, Amber is more important than her promise to her father never to take off the amulet. That's heartwarming enough, but then Amber turns Sofia down of her own accord, having a change of heart at the last minute. After all, it was Amber who lied and cheated to win, so it wouldn't be fair to make Sofia give up something.
The end of the two-parter "The Floating Palace" when both humans and mermaids are getting along well.
Sofia: I'm glad everyone's getting along.
Oona: Me too! It means we can be friends.
Sofia: It means we can all be friends now.
The end of "Holiday In Enchancia", with Sofia, Amber, and James giving their Wassailia presents to the peasant family who has given them shelter from a blizzard. Also when Sofia and Amber hug each other during the ending song.
After defeating Miss Nettle in "The Enchanted Feast," Sofia and Cedric share a brief but sweet hug.
Despite being a source of discomfort for Sofia, seeing Amber and James so eager to spend Mother's Day with Miranda in "Mom's the Word" is very sweet.
In "The Silent Knight," Aunt Tilly shows that she doesn't have problem with Sir Bartleby's voice, telling him she likes "one-of-a-kind things."
Cedric finally proving himself a capable sorcerer, thereby earning his perfectionist father's respect, in "Mystic Meadows."
Sofia and Hildegarde's friendship in "The Princess Stays in the Painting".
A very minor case, but in Hildegard's sad flashback, we see her big sister, who not only invited little Hildy to play with her, but showed concern when she fell down instead of laughing at her like everyone else. It's nice to think that someone as self-conscious as Hildegard might have a Cool Big Sis in her life.
Similar to "Baileywick's Day Off," we see that Sofia and the Royals fully consider Baileywick a member of the family in "Baileywhoops." To elaborate, when Baileywick keeps messing up (no one knows it was the cursed pin yet), no one scolds him or even gets mad at him, only suggesting he should take a break. Sofia does everything she can to help him do better, even promising to do his chores just so he can stay. That's dedication.
Also in that episode, Cedric makes peace with a former class rival, Greylock, and the two work together to save the assembled royals. And Greylock makes sure that Cedric gets his due credit for it, earning a round of appreciation from Roland, something Cedric clearly appreciates.
Everything concerning Sofia and Amber in "The Curse of Princess Ivy", especially Amber Taking the Bullet for Sofia.
Throughout "Winter's Gift," Sofia tries to find a special gift for Cedric. In the end, Sofia gives him a homemade wand case, and he's absolutely delighted.
So much so, that he uses a spell to summon snow for Wassalia, essentially the same type of spell he complained about as a "parlor trick" in the pilot movie, but here he does it gladly and without complaint.
Cedric coming to teach Sofia's magic class in "Substitute Cedric." Naturally, the sorcerer only agreed to it because he needed an herb from Royal Prep's greenhouse, but by the end of the episode, Cedric has had so much fun with the kids that he continues the lesson.
From the same episode, we see Cedric as a child, and he is adorable!
When Cedric learns that Sofia has been granted an invite to meet Merlin, his idol, he doesn't even express jealousy, telling her with great enthusiasm that she's been granted quite the honor. The scene only gets all the more touching when Sofia says that the invite allows her to take two guests, and since she knows how much Cedric idolizes Merlin, he was the first person she thought of.
"Dads and Daughters Day" has Sofia doubting if King Roland is her real dad, since he is her stepfather. During a school field trip with Roland and Amber, Sofia ends up feeling increasingly like a third wheel. Luckily Roland and Amber are both adamant that Sofia is Roland's real daughter even if he wasn't there from her birth and at no point is she considered just a stepdaughter.
Sofia discovering Roland's pocket watch has two pictures in it: One of Amber and James, which she saw first, and another of her.
"Camp Wilderwood"has James and Wendell legitimately getting along.
"Elena And The Secret Of Avalor" has many including, but not limited to:
Elena being reunited with Isabel and their grandparents
Elena hugging Sofia after being freed
Sofia encouraging Elena by saying that she's not alone
The Royal Family and everyone in Avalor helping Elena overthrow Shuriki
Sofia finally revealing the secret about her amulet, and the family being cool with it.
"Lord of the Rink" has Prince Hugo's father, King Garrick, doing everything he can to spend more time with his son,including becoming the assistant ice hockey coach. After seeing Sofia and Hugo perform in an ice-dancing recital, Garrick goes up to the pair, expected to reprimand Hugo for disobeying him only to exclaim that his son has done a wonderful job. Despite having said that ice-dancing was for girls, Garrick admits that he's proud of Hugo and hugs him right in front of an audience and Hugo not only sincerely enjoys it but isn't even embarrassed nor does he remind his father that people are watching. To top it off, Garrick even makes his decision to be the assistant ice-dancing coach.
"Day Of The Sorcerers" has a few stand out moments:
Sofia seeing the good in Cedric even when he betrays her.
Cedric can't bring himself to hurt Sofia even after taking over the kingdom. His heel face turn at the end makes this sweeter.
The royal family finally showing respect to Cedric is very touching.
"The Mystic Isles" has a few noteworthy moments:
Amber's song, "That's Not Who I Am", starts as a tearjerker about her thinking she's not a real hero, with Sofia reassuring her otherwise, brightening her mood. It really shows the depths of their bond.
During the climax,Prisma tempts Amber to join her instead of smashing the stone that would undo her magic and get rid of her new amulet. Amber than turns her down with the aforementioned smash. It also counts as a Crowning Moment Of Awesome.
"The Flying Crown" has plenty including, but not limited to:
Axel helping Hugo feel better (or trying to) after boasting to him about his flying derby days at Royal Prep
Sofia's warm talk with Hugo after Electra tells her what has been bothering him
Sofia telling Hugo what it means to be a champion as the crowd sings the Royal Prep cheer "Huzzah! Huzzah!"
Hugo and Sofia smiling at each other just before the race starts
Electra being nice to Minimus and saying, "That's the first nice thing I've ever said to you, but it won't be the last."
Axel saying that Hugo takes after him only for his little brother to sincerely and happily say that he takes after Sofia which makes her blush
Axel isn't even hurt when Hugo says this.
"The Tale of the Noble Knight" has Sofia meeting Willawing the dragon and her friends. Willawing finds Sofia adorable to the point where she just picks her up and hugs her and gently tickles her chin, which makes Sofia giggle adorably.