When Ray gets home after the aliens' first attack, he's in a total state of shock. His kids keep asking what happened, clearly scared, and he can't even answer.
Rachel freaking out in the car, as she witnesses the start of the attack.
"What do you mean?" Dakota Fanning's delivery of that line is amazing.
When the car gets stolen, and Ray and his family go into the diner and just collapse in a state of hopelessness. Even Ray starts crying.
The scene where Ray sings "Little Deuce Coupe" as a lullaby to Rachel.
Also their entire conversation leading up to that.
Ray asks Ogilvy if he lost anyone. Ogilvy replies, "All of them."
Rachel singing "Hushabye Mountain."
Ray's reaction when he realizes that he has to kill Ogilvy. He makes his way back to Rachel, then rushes up to her and hugs her tight. The look on his face says it all.
During Ogilvy's rant while Ray is preparing himself to kill him, he desperately insists that the Martians can't survive for long on Earth. Ray still has to kill him, so it doesn't change anything, but it's a lot harder to take knowing he was right.
The military attempting to make a stand against the tripods. They throw everything they have against the aliens to no effect and even admit to themselves they're only there as a distraction. And then they charge...
Ray and Rachel's reunion in the tripod basket. The way he keeps repeating her name, while she's in a total state of shock... Then, finally, she recognizes him and whispers, "Dad?"