What a great question! In first looking at the two novels, there might not seem to be many common themes, but there are. In fact, there are at least two: the theme of secrecy and the theme of childhood tragedy.
Let's take the theme of secrecy first. In The Lovely Bones, Susie Salmon is raped and murdered in the early seventies. It is, of course, the character of George Harvey who has the issue with secrecy. Being a serial killer who lures Susie into his makeshift abode in the middle of a field before raping and killing her, he must keep his actions, his place of operation, and in fact his life a secret. Here is how the secret ends up affecting George Harvey:
A moment later, the icicle fell. They heavy coldness of it threw him off balance just enough for him to stumble and pitch forward. It would be weeks before the snow in the ravine melted enough to uncover him.
He lives as "a neighbor" to everyone in Susie's neighborhood and seems to be a very innocuous person, but lives with a big secret. In The Memory Keeper's Daughter, the theme of secrecy is based around the life of Dr. David Henry. When his wife, Nora, has twins (which was unexpected) and one of the twins has the tell-tale signs of Down syndrome, David THINKS he gives the daughter away to an institution. (The truth is that Caroline, a nurse at the hospital, raises Phoebe on her own.) David then tells the family that the baby girl twin has died. This secret tears their family apart.
Now let's approach the theme of tragedy from a parental point of view. In The Lovely Bones, Susie Salmon is murdered and the family goes through all of the typical emotions of horror, grief, anger, acceptance, etc. Susie's death doesn't tear the family apart, but affects the family to no end. In The Memory Keeper's Daughter, the theme of parental tragedy is based on the supposed death of the girl twin (which isn't reality) and the secret that David keeps from the family. Nora goes through all the grief and anger about her daughter's "death," but then finds her husband has locked himself into an emotional prison. Why? Not only because of the guilt of the secret, but also because of this fact that Caroline is finally able to tell him:
You missed a lot of heartache, sure. But David, you missed a lot of joy.
Meanwhile, David loses himself with his music. David's secret absolutely destroys the family.