The scene with Alex and his mother in the prison and the revelation that she did love him after all, but tried her best never to show it due to knowing they would have to sacrifice him. Her last words to him? "I love you." Also a massive Tear Jerker.
Alex forgiving his father in the church is both this and a Tear Jerker.
Adam: I took my role as a father and I turned it into a daily chore. Fed him, cleaned him, and put him to bed. I treated the dog with more respect. And when I was given a second son, the first might as well have been a stranger sleeping in our house. Alex: I feel that you could start loving your son at any time. Adam: I do love my son, Father. I love both my sons. But I had to make a choice, and the only way to live with that was to make sure my son never loved me. I had to make sure that he would never feel joy or compassion, all the things that make life worth living. You must understand, I was only trying to make things easier for him... and for me. And for this selfishness, I ask forgiveness. Alex: If you truly want forgiveness, then you already have it.
The flashlight Alex uses the one he gave to Josh as a night light. Becomes a Tear Jerker when Alex gives it back to his little brother.