The concern on the Red Queen's face when the Grendel mentions the Knave to Jafar. It shows that no matter what's happen to her, she's still Anastasia somewhere inside her.
Will's talk with the Grendel and the honest sympathy he shows him.
Episode 4- The Serpent
More concern for the Knave from the Red Queen, even to the point of trying to send him back to Storybrooke safely. And in a more unexpected turn, she even shows concern for Alice when Alice is being magically tortured by Jafar.
Episode 5- Heart of Stone
The Red Queen pulls a Kick the Dog in both the past and present...but ends the episode with a major Pet the Dog of restoring the Knave from being a statue.
The Old Prisoner refusing to free himself because he would only get in Cyrus' way, and he wants Cyrus to reunite with Alice.
Cyrus being the only one to trust the Red Queen when she's begging to be trusted, because he can "read people" and is able to tell that she isn't truly evil.
Alice: I will never trust you!
Knave: Neither will I.
Cyrus: I do.
The Red Queen's whole motivation qualifies: she wants to break the Laws of Magic in order to change the past so that she never makes the mistake of trading love for wealth and power.
Anastasia: I'll give up my crown, I'll give up everything...everything, just to go back to a time when you love me!
The White Rabbit reunites with his family.
The Knave finally gets his wish: he uses it to save Alice and free Cyrus from being a genie so that Alice can be with him. Compare to the first episode where he only cared for himself and scoffed at Alice's love for Cyrus. For someone without a heart, he's come a long way.
Episode 9- Nothing to Fear
When Anastasia sadly says that nobody cares enough to pay ransom to save her, Alice and Cyrus come to the rescue, with Cyrus declaring "We would!"
Anastasia sincerely thanking them for the effort, even though it didn't work.
Episode 10- Dirty Little Secrets
Tweedle coming out of nowhere to help Anastasia. Especially after the last episode where she said that absolutely no one at the palace would ever try to save her. Especially heartwarming is her face when his answer for why he would save her is just because she is his queen.
Episode 11 - Heart of the Matter
Alice has finally gotten over her hate of the Red Queen. When she sees her behind bars and hears her emotionally say "Thank you for coming back. I know you didn't do it for me but thank you!", Alice tears up and actually calls her "Anastasia".
When Jafar takes Will's heart and tries to kill Cyrus and Alice, his staff fights back. That's when Cyrus realizes that the staff is actually his mother.
Episode 12 - To Catch a Thief
Alice decides it's wrong for her to use Will's heart to force him to help her find proof of Wonderland for her father and gives him the heart back, no strings attached. Will stays to help her anyway.
Will sees Alice as how his dead younger sister would have grown up to be like. Awww...
Episode 13 - And They Lived Happily Ever After
Alice and Cyrus getting married in her father's home, with Will, Anastasia, both Rabbits and the remaining non evil Tweedle attending, and the White Rabbit presiding. Edwin, Alice, Sarah and Millie are all united and Edwin couldn't be happier to introduce Cyrus into the family.
The fact that Anastasia is wearing light purple. Light purple is the opposite of dark red on the spectrum and (apart from white, which she cannot wear due to Alice being in white) is the closest thing to "purity" she can get, showing the truth of her change.
The big bear hug Alice gives Will thanking him for everything he's done for her.
The entire series really started with their friendship... and together, both of them managed to get back the true loves they thought they'd forever lost.
Will and Anastasia getting married and becoming the White King and Queen of Wonderland.
The ending with Alice reading the story of her adventures to her daughter, while the White Rabbit looks on smiling in contentment.
The scene where Anastasia is revived; not just the look on Will's face, but the fact that the music rises to the loudest crescendo the show has ever had, it so heartwarming. Then, Anastasia's reply to Will informing her that what happened is "a bit of a long story" - she merely asks: "Are you sure I have the time to listen?"