The ransom note: The paper came from within the house. It was the longest the FBI had ever seen at 2.5 pages. It stated a demand for ransom in almost the exact amount of John Ramsey's Christmas bonus. Also, the writing sample Patsy Ramsey gave matched the writing on the ransom note. In my opinion the note came from an educated person, not some thug who was trying to kidnap the girl for monetary purposes. "Foreign Faction?" Is an odd thing to call yourself, if calling yourself anything at all.
There were no signs of forced entry in the house. No cobwebs were even disturbed on the basement window. The house was massive, at four stories and someone would have had to know the layout to find the basement and place her there.
She was initially comatose from blunt force trauma, but the killing occurred from the strangulation. The garrotted paintbrush which required a knowledge of knots to be able to make. John Ramsey was a sailor and knew how to tie such knots.
Her favorite food, pineapples were found in her stomach which she consumed shortly before her death.
Traces of urine were found on her nightgown and in her bed. As well as evidence of damage done to her hymen to indicate sexual abuse. Some people believe she was punished for wetting the bed. An accident that turned fatal, but why not call the ambulance in that case and say she's hit her head or something?
Police Chief Mark Breckner talled about "Occam's Razor Theory" in his AMA which basically states that the simpliest solution is usually the right one.
Personally, I believe the parents covered it up but it could have been her brother that accidentally killed her in a rage. He was having bed-wetting issues as well which can cause embarrassment ,frustration, and lashing out. He was a kid at the time, but one of his therapists released a documented report about Burke's strange behavior in regards to his sisters death. Could have just been he was in shock or turmoil. The dad may have also been molesting his daughter and she may have screamed or said no and then he got angry and killer her and his crazy wife covered it up.
However, an intruder is certainly possible considering the Ramsey's entertained a lot, and had tons of people coming and going from their home.