The chaste, bittersweet romance between Joe and Alice.
Clinched by the scene in Joe's bedroom where Alice watches the Super 8 film of Joe's mom filmed from Joe's birth onward, as both kids are coming to terms with how their two families were devastated by the accident that killed her.
When Joe's father finally finds him and gives him that hug the Sheriff said he should.
And when Alice and her dad hug as well.
When the alien looks at Joe, really looks at him, and understands what he's saying. And they both get to go home.
The very ending of the film, where Joe finally lets go of his mother's necklace, symbolising him coming to terms with her death, and the alien's spaceship lifting off into the night sky.