The Signs in the Silence - S6-E21
Stupidity: Bones realises she could pull a wisdom tooth from Amy in order to identify where she grew up and find her birth parents. Which works, but at no point do they consider simply going through missing person records with the relevant info. They know how old she is, they know roughly when she disappeared, not like there are hundreds of 3 year olds going missing every year, especially not with Waardenburg syndrome. By that age her deafness would have been apparent, which would narrow the pool hugely.