The hardest part about this is that it's broken up into basically three divisions. Additionally they do have several characters aside from these three belong to.
Division one: Grow up alone
Basically Naruto's childhood is one where he has no parents...additionally he's a jinjuriki so he had uncalled for hatred blamed on him.
Additionally you have people such as Kabuto who grow up as an orphan.
Going further as an orphan you could have Nagato who is an orphan in a war zone.
Division Two: Murdered Family
While not as severe, you have people like Neji who's father was sacrificed/murdered. While it protected the village... It obviously is still to grow up knowing your father was killed.
In theory you could go higher and with Iruka have both of your parents killed, and then have to teach the Jinjuriki of the Bijuu responsible...not to place hate on Naruto so much as Obito or Kurama.
Finally we have Sasuke...enough said.
Third Division: Family Hatred
Starting off not as severe, we have Hinata who, while she has family, they look down on her and found her expendable (Hiashi, Elders, Neji, possibly Hanabi).
You go worse when you have Gaara who faces the exact same thing; however, his family tries to kill him... A lot
So really it depends on which division of a bad childhood you find to be the worst. Personally, I go with the third one. I'd rather have no parents, or have them sadly pass away on me as opposed to actually have a family, but they hate me.
So I go with Gaara.