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.
