I just finished reading Foreign Faction - Who Really Kidnapped JonBenet? by A. James Kolar. While it is the only book I have read on this case, I believe the author was very thorough and objective in his analysis of the evidence.
To cut to the chase, the probability of an intruder sneaking in to the house and murdering JB is slim to none. It was almost certainly a story invented by John and Patsy Ramsey. As for “who done it,” it is hard to say, but the most likely suspect is Burke. He killed JB, either by accident or purposely, and his parents covered for him. John and Patsy Ramsey were also very wealthy and influential, and had the DA’s office in their back pocket and used the media to their advantage.
Sadly, there is no direct evidence or proof that John, Patsy, and Burke Ramsey were complicit in the crime. Unless John or Burke confesses, it is doubtful a conviction will ever materialize.