All I can remember is that there's a young boy/girl? Who is somehow separated from his family (they might have been killed) and has a wooden doll that can transform. I also remember it being kind of dark or anime like. Thank You to any one who has any ideas.

Wild guess

Maybe the puppet wizard Lord Kuruku
And the little girl Cherri from,.

Unico: In the Magic Island

Unico the baby unicorn meets a little girl named Cherri (Sherri).Cherri's older brother had run away from home. When he returns he is the apprentice of an evil puppet wizard who has a plan to turn all of humanity into wooden puppets, to get revenge for being abused and abandoned.Cherri's brother Toby spares his little sister by hiding her from his master. After Toby and his master the evil puppet Kururu leave, she and Unico go on a quest to the ends of the earth to find the all knowing Trojan horse. It's said that it should know of a way to turn her family and friends back

Kuruku is eventually defeated when Unico shows him love instead of hate. The hatred that animated the living puppet left him and he returned to being a normal wooden doll/puppet

Thank you, after reading your description I remembered a bunch more and your absolutely right. I've been asking people about this for years and no one had any idea.