In the flashback, Neville's daughter gives him Sam saying the puppy will protect him. It gave Dr. Neville a friend in his isolation, and indeed Sam saved him though at the cost of her own life.
The film's alternate ending. The reunion between the Alpha male Darkseeker and the female is almost indescribably tender, and very powerful.
Also in the alternate ending, Neville going with Anna and Ethan to the survivor's community. Three years of desperation and loneliness and bad deeds with good intentions, and Neville can finally be with people again.