I was unfamiliar with the case. After checking out both links for quite some time, but prior to reading the comments, I estimated:

1. 80% (Knox)
2. 60% (Sollecito)
3. 95% (Guede)
4. 90% (confidence in coincidence)

After reading the comments, I was a little surprised that the consensus seems to be decidedly against Knox's guilt. The simplest explanation is that I'm just not a very good rationalist, but I don't find that very satisfying. The four parts of the story that I felt were inconsistent with Knox being innocent were:

1. Knox's initial account of the night. I tend to believe confessions; it's a weakness of mine. With the exception of the wrong black man being implicated, I think the major thrust of it was true. Complete innocence would mean that the entire account was made up, which seems hard to believe, even if under heavy police questioning.
2. The bra was removed after Kercher's death. Would Guede have done that? I think that evidence is much more consistent with someone cleaning up after the fact.
3. The body was covered. This is inconsistent with the actions of a rapist/murderer, but very much what you would expect of someone who had a close relationship with the deceased.
4. Knox did not flush the toilet. She says that she noticed that the toilet contained a deposit, yet she walked away without flushing. Why?

I'm not sure what role Knox had in Kurcher's murder, but I feel very confident that she (and likely, but not necessarily, Sollecito) knew about the murder long before the police were called, and moved to cover it up. I can't see that as anything other than a sign of guilt, unless my understanding of the evidence itself is wrong (which is certainly possible). I can understand if some feel the need for the motive to make sense to find in favor of guilt, but according to Knox's initial account, she was stoned at the time -- which lowers my personal threshold for the expectation of rational action.