DNA from the panties; hair
In 1999 a reporter for the Denver Post
wrote, "But the most powerful evidence pointing to a killer outside the Ramsey family was a stain of body fluid inside the dead girl's panties. The stain carried DNA that police can't link to anyone...Much supposed evidence in the murder has been leaked by anonymous sources; there's no independent way to verify if the leaked information is true, or subject to different interpretations, until the case goes to trial...Other evidence pointing toward some outside intruder includes an unidentified pubic hair found on the blanket wrapping JonBene�t's body; a Hi-Tec hiking-boot print discovered near the body that hasn't been matched to any family or friends; a broken window in the basement where JonBene�t's body was found; and an unidentified palm print on a door by the girl's body."
The relationship between a stain and a DNA sample is never "implicit," to use Professor Peter Gill's words. Other article have said that this DNA was sub-source. If this DNA did in fact arise from a stain, then its evidentiary value is greater. I do not know whether the hair mentioned above was tested for DNA or not. At
Reddit, it was argued that it was not a pubic hair and that DNA testing was done. The article makes a good point about most of the information as of 1999 having come from leaks.
"There are no do-overs in crime scene processing. “You only get one chance to do it right,” says Joseph Giacalone, a professor in the Department of Law & Police Science at John Jay College of Criminal Justice. Giacalone, a former New York police sergeant who has worked on hundreds of murder, suicide and missing-person cases, says that securing a crime scene and properly collecting and storing evidence is crucial for prosecuting a court case."
link.