You know, I keep seeing people wondering why the brains are being taken, and I just think it's bloody obvious.
Mohinder said in the very first minutes of the pilot, how if mankind could just access even one more percent of their brains, they would become closer to god, maybe gain powers.
So, it's pretty clear to me that the person doing the killings is poking at brains to find out just what makes them different, what little switch in the skull activates those powers. The ultimate purpose is still a mystery, but it's probably to duplicate them in some manner.
"Is he a zombie??" NO!