Before they set on their plan by having Ellen pose as a Johannsen daughter in case the Nazis came (using Lise's name), Mr. Johannsen kisses both Annemarie and Ellen on the heads telling them "Don't be frightened. Once I had three daughters. Tonight I am proud to have three daughters again."
The chat about Lise that Annemarie and Ellen share, with only child Ellen telling Annemarie that she used to pretend Lise was her older sister. Annemarie tells her back that Lise would've liked that, since she loved her too.
Peter still keeping a close relationship with the Johannsen family even after he lost his fiancee/their daughter.
Many of the Gentile Danes making sure that their Jewish friends and neighbors will be taken care of and it's revealed that they've kept their departed neighbors homes clean for them.
The end of the war
Kirsti has grown up into a tintype of Lise, with a brighter and longer future
Mr. and Mrs. Johannsen confiding to Annemarie that Peter and Lise were members of the Resistance
Annemarie getting her father to fix Ellen's broken (and up until now) broken Star of David necklace, which she will wear around her neck until Ellen gets back.
Mrs. Johannsen looking after Ellen, reminding her not to feel bad about her hair color (nearly gave the family trouble with the Nazis) and to tell Uncle Henrik that they've brought a friend (Ellen).
Ellen's reunion with her parents
Uncle Henrik telling Annemarie not to worry, she will see Ellen again
The short but sweet moment where Mrs. Johannsen brings a Jewish baby, Kirsti's sweater, and the Mother tells Mrs. Johannsen that the baby is a girl named Rachel.
Ellen reassuring Kirsti, after the younger girl is distressed for having green fish skin shoes (leather was scarce in the war), that she will take the shoes home and get them black and shiny with her Father's help. The Rosens and the Johannsens indeed have a close familial relationship with one another.