I think the most important bonus scene is after the wedding when the Don takes all of his sons (including godson) to see Genco in the hospital. Without it, one never understands how Tom becomes consigliere. Remember, at the wedding, Michael tells Kay that Tom is going to become consigliere, but there's no way of knowing who is then the consigliere, or how Tom actually moves up. Also, when the Don comes home from the hospital, and Sonny and Tom have an argument on their way downstairs, Sonny yells, "Pop had Genco, look what I got." Unless you read the book, or see this bonus scene, or watch GF2, you have no idea who Genco is. Finally, when the Don asks Michael about the "Christmas decorations" on Michael's uniform, it sets up the tension between the Don and Michael, while Michael is still an outsider.

For these reasons, I think this scene, of all bonus scenes, should have been part of the body of the movie. Other bonus scenes, while they add to the story, are not so vital to the story as this one.