The dedication of Mikael's book exposing Wennerström reads: "To Sally, who showed me the benefits of the sport of golf."
We don't see it in the book, though we do in both film adaptations: the reunion between Harriet and Henrik.
Lisbeth telling Mikael that she likes working with him and him responding in kind. Aside from the major breakthrough that such a declaration must be for her, it's sweet to see the genuine mutual respect and admiration each have developed for each other.
A moment cut out of the movies: Blomkvist tells Berger that Salander is the person who saved him from being killed. Erika glomps Lisbeth.
The Girl Who Played with Fire:
When Mikael writes a message to Lisbeth promising that they can solve the case together, she writes back "Thank you for being my friend."
Lisbeth's relationship with her previous guardian, Holger Palmgren, who is one of the few she truly trusts.
Lisbeth inherits a rather small amount of money after her mother passes away—a mother who was crippled by brain aneurysms and often could not recognize Lisbeth at all, nor tell her from her sister Camilla. She donates it to a trauma center for women: "She wanted to spend the money on something that would have made her mother happy."
The Girl Who Kicked the Hornet's Nest:
Lisbeth finally getting her happy ending and having her declaration of incompetence rescinded.
When Mikael and Lisbeth reconnect
Armansky, Blumkvist and Erika celebrating at the end.
Lisbeth visiting Miriam at the end
Palmgren being a defence lawyer for Lisbeth, despite not fully recovered from his stroke, also a Crowning Moment of Awesome. He was a good man, we see why Lisbeth trusts him.