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 white 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 sorceror 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.
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 Echancia", with Sofia, Amber, and James giving their presents to the peasant family. 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.
Cedric finally proving himself a capable sorcerer, thereby earning his perfectionist father's respect, in "Mystic Meadows."