It's hard to choose how suffered most, as you can't really rank suffering on a scale. I'll just say these people tie.
Sasuke: Where do I even begin. Life is going fine until you come home one day to fine the corpses of you family on the ground, and then your loving brother turns out to be the monster who killed them, who then mind rapes you. All this at 7 or 8. Brother comes back again 4-5 years later and mind rapes you once more. You make a life goal and then find out that your brother actually loves you and your family dies just so other people can be happy. The loss of his family is made even worse simple because as an Uchiha, he loves more than a normal human being, and so feels even greater pain when he lost them. This isn't even the full story. That's a sucky life, not just a sucky childhood. I'd have commited suicide by now.
Naruto: Everyone hates you for a reason you don't now and because of something you can't control. They've hated you since you were born. No parents or siblings. No one to share anything with. Having to cause mischief just to get someone to scold him. It gets turned up when he finds out there's a demon in his belly. Makes me want to cry when I think about it. Then Sasuke leaves. Poor thing.
Kabuto: Tricked into killing his own mother. Never even knew who he was.
Itachi: Killed his own family and lover, ruined the life of the one he loved most. Tragic, but he gets less sympathy from me because it was stupid to kill people who wanted nothing but rights.
Nagato: Just one disappointment after the other. First his parents, the Yahiko.