I have never cried so much during a movie (or in general) as I did during this! I started crying when he was lying in his closet (?) and listening to the message from his father on 9/11, we saw the marks on his ribs, and while he lay under his bed. Five minutes after I'd finally stopped, when he started fighting with his mom about burying an empty coffin, and when the mother talked on the phone with his father during 9/11 cried again. And then, when he showed his grandfather the messages, and talked about the last message with Mr. Black, and finally broke down I also cried. Basically, I cried throughout the entire movie..
I was sad generally throughout the whole movie, and once in a while I'd start crying (After Extremely Loud.. this is the most I've cried from a movie) Especially when she died I saw it at the cinema, and during the credits, which were completely silent, most people stayed seated (which is really rare) and I could hear several people sniffing..
In the scenes without any talking, with just music. Especially at a couple minutes into this scene, and also every time he looks at a picture remembering Ellie. And also at the end, when he sees the last pictures in Ellie's adventure book
Warning: The end of the movie is shown at the end of this clip, starting at 6:04, the rest is from the very beginning