If he did it there will be some interesting fall-out. According the the online story I read he confessed to drugging the girl and then sexually abusing her. However, the reports at the time were that no drugs or alcohol were found in JonBenet's system. An investigator said that some details about the killing were not released (which is always true) but what about releasing false information? I dunno, just from the news stories it sounds like this guy is one sick puppy who had read everything there is to read on the case and has placed himself into the picture. A good defense attorney will get the confession thrown out. The only evidence that will convict will be the DNA evidence - and I have heard the same arguments as listed above - it is so corrupted that it may never even see the light of trial.
All that being said, if this is the perpetrator, thank goodness they finally caught him.