4 things that sink the intruder theory for me
The Grand Jury
In GJ hearings, the prosecution presents its case. In a highly unusual move, intruder theory evidence was presented to the Ramsey GJ. They found the intruder case uncompelling and indicted the parents. Alex Hunter then hid the indictments for several years until legal action forced him to disclose them.
The Stun Gun
While the physical evidence seems to indicate the use of a stun gun, and a stun gun works well in intruder theories, the fact remains that no actual stun gun manufactured matches the marks found on the body.
The Phone Records
When detectives finally got access to the phone records, the one for December was wiped clean. This is unheard of. It indicates the intervention of a person or persons with enough power to get the records erased and remain anonymous in doing so. A cover-up indicates the existence of something to be covered up and Ramsey motive to conceal key evidence.
The Lack of Footprints
I'm tired of the bogus arguments about this. There was a light dusting of snow in Boulder on the night of December 25-26, and the temperature did not rise above 7*F till after dawn; i.e., the snow did not melt away overnight. The light snow did not stay on the walkways around the house because they retain more heat than the ground, and the 25th had been warm (mid-50s F, IIRC). The snow did stay on the ground immediately around the house and on the snow still on the ground from an earlier snowfall. The strip of grass around the grate over the train room window was one of the places where the overnight snow remained undisturbed. This was observed and reported by police first on the scene. The lack of footprints in that area and in the snow around the rest of the house, plus the lack of forced entry anywhere that could have been accessed by a walkway not covered with snow, indicated that there was no intruder. Photos have circulated online showing grass around the grate not covered in snow. These have been used to bolster the intruder theory but do not in fact do so because they were taken later in the morning after the temperature rose and the light snow had begun to melt. Had there been an intruder in the night, there would have been footprints in the snow when police first arrived.