Hey, I am new to this site so I thought I'd post a little something about my thoughts on the case. ( I apologize if these points have already been spoken on, feel free to ignore this if they have)
Something I recently learned about was that a few months before JB was murdered her brother had hit her in the head with a golf club because he was mad at her. I've always thought that the brother had done it and the parents had covered it up. This sounds like a child with anger issues, and I believe that he could have killed her in a rage.
When talking about the incident, Patsy also changes her story to make Burke sound younger. (She says the incident happened in 1993 when it happened in 1994. She also says that he is 2 and a half at the time, which was also incorrect). She also downplays the injury that JB received. It definitely feels like Patsy is trying to cover for Burke's anger issues.
I have a little theory that Burke was angry at Jonbenet, possibly because she took his pineapple or was eating it. I think that because Patsy, Burke and Jonbenet's fingerprints were found on the bowl it is possible that Patsy had gotten Burke a snack, and went to another room. Jonbenet came in and took the pineapple, which angered Burke.
Burke lashed out and killed her. The mother wrote the ransom note, while the father tried to make it look like a kidnapping. I believe Patsy was in the same clothing as the night before because she hadn't slept that night. She was up writing her 3-page ransom note.
As for the unknown DNA found in the underwear, and this is a THEORY, but it is possible for unknown DNA to be found in brand new underwear (or any clothing). This has been tested before and sometimes DNA is found in clean, unused clothing because it is not sterile.