My theory is this: I agree with the first post on this thread, that the note was written by someone educated, etc. But I don't think it was the Ramseys. It's a very long note. In a panic, I can't imagine anyone writing something as involved as that. Also - why would they even bother with that? If something had really happened to her and they wanted to hide their culpability, it would make more sense for them to try to get rid of her body. There was no inkling of psychopathy in either of them, and what was done to their daughter was so brutal I can't imagine anyone doing that to their daughter without severe mental issues, even in anger.
I think that whoever did it either worked at John's company or knew someone (girlfriend? wife?) who did. That person was somehow aware of John's bonus. He had been watching JonBenet for awhile and planning to abduct her. He may have been at that Christmas party they threw and saw the lay-out of the house - maybe that event gave him the incentive to implement a plan at that point. I think he broke in and took JonBenet (wasn't it thought that a stun-gun may have been used?) I think he wrote the note ahead of time with the idea that if he left it, the police would be looking for a kidnapper, not a pedophile. He left the note and proceeded to try to get her out of the house, but wasn't able to. So he assaulted her there (and maybe because that wasn't part of the plan, he was unable to keep his dna from being left behind on her underwear) and killed her, both hastily. But the only way to really check out my theory or at least parts of it would be to take a look at the employees and figure out who might have been privy to the information about the bonus. The note used the word "fatcat", which, to my understanding, is a negative word for a rich person (there's more to the definition than that) possibly indicating resentment towards John, which someone in the company might have. Perhaps it was the wife or girlfriend of someone who would know and he pumped her for information. Just a couple of ideas. (Since I'm new to all this, it's probably already all been said and discounted! But I'd love some feedback!)