For me, the failure to document the controls was huge. And then the farce of the prosecution claiming that they existed and not having them in their hand. Huh, a cornerstone of your case is the reliability of the DNA testing and you decide to come to court without copies of the documentation of the control experiments and then when the documentation is produced it is not the documentation for the test in question? So an outside observer needs to choose between wildly incompetent prosecutors or just dishonest prosecutors?
And a small issue that might seem more important to me than it actually is. Stefanoni threatened to sue the experts that criticized her. Huh, on what planet does that make sense? That suggests that Stefanoni might not be the brightest bulb. If expert witnesses can be easily sued because they criticize the prosecution's case then where are you going to find expert witnesses to ever challenge prosecution evidence? Unless she has evidence of significant malfeasance by the people that critiqued her actions and findings the threat of a lawsuit sounds like childish junior high blather to me, which would tend to indicate that she has a position that exceeds her capabilities and talents.
Negative evidence as I understand it.
1. False accusation - Sounds like coercion and perhaps language difficulties easily explains this. Testimony taken after forty hours of questioning might be useful as an investigation tool, but it should never be allowed into court without corroboration and it doesn't sound like there was any.
2. DNA on the knife
This sounds like it was completely shot down by C & V. So much so that it isn't even a useful piece of evidence in a preponderance of the evidence kind of case.
3. DNA on the bra clasp
Even after the C & V testimony it sounds like the evidence can not be completely discounted at least in a preponderance of evidence case. The mishandling of the clasp which conceivably could have led to cross contamination, the difficulty of correlating the evidence with the rest of the crime scene and the problematic nature of some of the police scientist's procedures easily makes it too suspect for me to be of value in a case to be decided based on a beyond a reasonable doubt criteria.
4. Other evidence
I am still trying to figure out exactly what of significance is left. I am just now finding some pro-guilt writing that seems to believe that there was a lot more evidence against Knox than the three issues I listed above. I need to work at understanding what they are before I know what to make of them.
This is a pretty good summary of where we're at right now. There is indeed other evidence that - if one goes with the prosecution interpretation - is significantly incriminating towards Knox and Sollecito. The main areas here are these (giving the prosecution interpretation, followed by what many of us here believe to be a more rational interpretation):
1) The mixed DNA in the bathroom sink/bidet: The prosecution allege that Knox's DNA and Meredith's blood DNA were deposited at the same time, meaning that Knox must have been involved in the murder. A more rational explanation is that Knox's DNA was already present in the sink and bidet, given that she used that bathroom regularly. Furthermore, the crime scene video clearly shows that the samples were not correctly collected using a careful dabbing technique: instead, the forensics official (who also doubled as the photographer!) clearly smeared wide areas - meaning that the dilute spots of Meredith's blood were potentially mixed with any other latent DNA that was present through the whole arc of the smear.
2) The "staged" break-in: The prosecution alleges that there is no way that the break-in could have been real, and that only Knox would have a reason to stage it. But the prosecution based this on the flimsiest of evidence, and apparently didn't even conduct a proper search of the ground below the broken window (this area of ground was used as a cigarette and phone-call area for the police!). The rational explanation is that the evidence found is entirely consistent with a real break-in, including the distribution of glass, the placement of the rock which broke the glass, and the presence of a hair which was probably Guede's on the window frame. Wonder what happened to that hair, huh.....?
3) The partial print on the bathmat: Prosecutors allege that it's possible to match this print accurately to Sollecito,, and to actively exclude it as a match to Guede. A rational explanation is that it's essentially impossible to say that the print is anything other than the dilute-blood print made by an adult male with above-average foot size. The prosecution's "expert" conducted a suspect-centric examination of the print, and it appears that he deliberately chose his measurements to match those of Sollecito's reference print. The reality is that the print on the mat is made on a tufted, textured towelling mat with a saturated blood/water mixture, making precise measurements totally impossible. The rational conclusion is that the print is almost certainly Guede's, but at the very least it cannot be positively attributed to Sollecito. In addition, Massei's "reasoning" came up with this gem: the print contained Meredith's blood; Meredith's blood was only present in her bedroom; therefore whoever made the print bot the blood onto his bare foot inside Meredith's room, and walked to the bathroom; and therefore the absence of similar bloody prints between Meredith's room and the bathroom is evidence of a post-crime clean-up!! The rational explanation for this is that the killer hadn't stepped in blood at that point, but went to wash blood off his clothing in the bathroom (the print was clearly made in a very dilute blood/water mixture, so it wasn't made by stepping directly into Meredith's blood anyhow). The killer placed his foot in a pool of blood/water in either the bidet or the shower while washing blood off his clothing, then stepped onto the mat.
4) The testimony of Quintavalle: The prosecution alleges that Quintavalle's testimony is reliable and accurate, and apparently Massei's court somehow accepted this. Quintavalle says that Knox came into his shop at 8am on the morning after the murder, and browsed in the cleaning products area. Since Knox claims she was in bed at Sollecito's apartment until around 10am, Quintavalle's testimony would be very damaging if true. But according to Quintavalle's employee, when the police visited shortly after the murder, Quintavalle didn't recall seeing either Knox or Sollecito - despite even being shown photos of the two. He only came forward with his story a year after the murder, at the "request" of a newspaper journalist. The rational explanation is that Quintavalle is either honestly confused (maybe he's retrospectively convinced himself that he really did see Knox that morning), or he's simply a liar. Either way, the way his testimony came to light clearly significantly affects its reliability and veracity to the degree that it's probably useless.
And there are other, more minor, areas that can be similarly discussed. The long-and-short of it is that there is simply no solid, reliable evidence that points conclusively (or even cumulatively) to the guilt of Knox or Sollecito. If I (or most people here) could be shown just one incontrovertible piece of evidence pointing at guilt, I'd have no problem changing my opinion. But no such piece (or pieces) of evidence exists - it's as simple as that.