Declan has the opportunity to destroy Adam's relationship with Charlotte with a video of him cheating on her, but instead just sends her a sincere request for a date, hoping she'll pick him as the nice guy over the Jerk Jock.
She might not admit it, but Emily seemed touched that Jack named his boat "Amanda" after her.
Pretty much the entirety of Jack and Nolan's conversation in "Treachery," when Nolan slyly approaches Jack to give him his boat back and tell him that he doesn't have to pretend to be Nolan's friend anymore only to have Jack apologize for being a jerk and fix him a drink.
Emily apologizing to Nolan and admitting he's her friend after all. D'aww.
Declan falling asleep while attempting to read Paradise Lost because it was on Charlotte's reading list. The boy may be The Scrappy incarnate, but he has his moments.
The Reveal that Carole Miller is Nolan's aunt - and he withheld the last journal from Emily to protect his family.
The death of Sammy, the curiously long-lived dog, was actually pretty moving.
Nolan trying to get Emily to come with instead of staying in the white haired assassin's basement to either kill him or be killed by him. Then unable to do that, hugging her and saying "Kick his ass."
After getting Charlotte out of rehab, Emily takes her to the beach, so she can meet Faux!Amanda, as a way of making her happy. Doubles as a Tear Jerker when you see that Emily is genuinely sad at the fact that she can't be her big sister, as much as she would like to be.
Just in case she wasn't totally unhappy about losing Charlotte, she also has to let Amanda take Jack, her childhood friend. And yet sometimes it seems like she wants them to be happy, knowing she can never have it.
S2E7: "Nolan, your company; everything you've worked for-" "Means nothing if it could potentially hurt the only real family I've ever had."
The flashback to Child!Amanda and Child!Jack's pretend wedding, with Sammy as the best man. Too adorable for words.
Daniel rescuing Charlotte from rehab and setting up an independent trust for her after she loses her inheritance.
Charlotte visiting Emily in the season three premiere, and they hugging each other, before Emiy genuinely comments on how great she thinks Charlotte is doing, before Charlotte basically drags her outside the house to watch the sunset with her. They sure act like sisters sometimes.