Hmmmm gotta go with the Elric brothers. They really went through hell. Though I'm not sure what's worse-being outcasts all your childhood like Naruto or going though major bouts of trauma and pain in one year.

........I think I'd take outcast over losing a mom, brother, and my arm and leg....

And Al...POOR AL!!! He can't even taste food, feel temperature or HUG somebody. That's got to be the worst.

Yoite!! :(

Gaara (I mean even his own dad tried to have him killed >_>)
Sasuke & Itachi Uchiha
Ed & Al Elric
Suzaku Kururugi
Zero

sasuke
naruto
kakashi

the elric brothers- they went through hell literally they lost there limbs trying to bring their mother back and they nearly lost their lives
robin one piece-okay this one is self explanitory for any one piece fan she was abused by her aunt barely fed outcasted by everyone else and entire town destroied when they found her mother came from it she saw the destruction and saw her only friend die(?) before her eyes thats tragic
erza fairy tail-some people call it a childs anime however when the anime reached that arc it changed quickly it was reveald erza was in slaved working on a tower to only revived ONE PERSON she went through hell for all her live she didnt remember her name or anything else she had some friends however during a breakout she lost one of them before her eyes she also lost another one her best friend she escaped but if she ever told anyone her friends would die she lived hell for all her live afraid to tell anyone until that arc.

Same here i go with ELric brotherss there childhood was hell

angel beats ! : yuri ; wanting to protect those most important to her , but couldn't . she stood there watching as they got killed one by one . T^T
myself ; yourself : nanaka ; she didn't really have the worst childhood , but it was kinda bad . ;\

key character backgrounds( clannad, angel beats)

Elric brother backgrounds

Lelouch background(just bad parenting)

Evangelion background(why did shinji turn out to be so emo!??)

Tamaki from Ouran...better yet, there's Naruto

seta soujiro from rurouni kenshin had a REALLY REALLY REALLY terrible childhood. =\

sasuke,
itachi
gaara
naruto

lucy

Himura Kenshin

I would have to say Robin of One Piece and Erza of Fairy Tail.

Thus far, I have to go with Lucy from Elfen Lied, personally I didn't like Elfen Lied that much, but Lucy's back story kept me interested because he's not like the rest of the ridiculous Elfen Lied cast, I actually felt sorry for her. Not even Naruto is that melodramatic(until the filler kicks in anyways) but not as ridiculous as InuYasha.

Erza Scarlet- Can you imagine a child haven't experienced to be a kid but a an innocent prisoner, and slave?
Sasuke Uchiha- How can you let a child see the deaths of the one he loves so much in his life with his own eyes?

I think it is Lelouch Lamperouge as well, because lol, being decieved for your whole childhood life with the ones you love? OUCH...
Elric Brothers as well... I can't stop crying seeing Alphonse Elric and Edward Elric being separated from each other specially after all that had happened between them. It is a painful part for siblings, lol.
I bet Kenshin Himura too. Because I don't know... XD

Well this might sound crazy but I want to include Hanamichi Sakuragi, and Natsu Dragneel. They are both the same for the pain they both feel. I mean they both lost their fathers, found a foster one, and wishing it to last forever. And man, these men are both tough!

Well if you have watched the animes which these guys are from, maybe you'll get to know more of their childhood story.