It was originally believed that Wendy had made her "Stray Dog" AKA Gregory kidnap the kids to test his loyalty, but this was later disproven by the dates of the kids disappearances.
Others still hold strong to the idea that it was Gregory who kidnapped the kids-killing them, grinding them up, and burying them. On the day of two of the missing person reports, Gregory's diary says he "planted peas", which some read as "burying the remains of a child". There is also the stuff in the bathtub that Jennifer states "almost looks like" blood, the three holes in the garden, and the morbid little rhyme that Gregory recites in the basement with a gun to his head. And then there is the fact that Wendy calls his house the "Gingerbread House", bringing to mind the house in the fairytale called "Hansel and Gretel", which belonged to a witch who would lure children to her house with candy, then eat them up.