I see a huge difference in looking at Rudy and Amanda/Raffaele. The evidence is very strong that Rudy killed Meredith and pretty much non-existent that Knox and Sollecito were involved.
Then we have to look at why Rudy killed Meredith. I see 2 potential scenarios. One that Grinder has suggested. That is that it was a date rape that turned into murder. And that Rudy smashed the window as a diversion. I think this is unlikely and without any evidence to support it.
The second, which is that Rudy broke into the cottage to steal and was interupted. His arrest in Milan for trespassing and possessing stolen goods from another burglary committed only days before is highly suggestive of a burglar. Is it enough to convict him of burglary in either event. I don't think so. But that doesn't mean that it isn't probable. It's like the difference between a civil trial and a criminal trial. One requires a preponderance of evidence and one requires beyond a reasonable doubt.
Now a difference that deserves some discussion is being put forward.
Why would Guede have attacked Meredith Kercher if she had merely interrupted another episode of "sleeping rough" as Grinder called Guede's trespass into the nursery in Milan?
Some (perhaps including myself) have speculated that the female nursery owner who discovered Guede in her nursery school was not attacked because she was accompanied by two males. The odds of a successful attack on her may not have seemed good to Rudy Guede.
Meredith entered her apartment alone, and may not even had been aware the Guede was there (if he was in the larger bathroom at the time). He may have surprised her in her bedroom. Or he may have heard her entry and surprised her before she reached her room.
If one followed Grinder's ideas (about the Milan nursery) of Guede seeking to peacefully trespass to perhaps sleep rough (and why would he do that in Perugia), why the attack on Meredith? Why didn't Guede simply explain to Meredith that he had entered her flat - to use the toilet, perhaps - and ask to be let out, or allow Meredith to call the police?
If a date rape with murder (which I would guess is rare), did Guede take Meredith's money to further the appearance of a break-in? It's noteworthy that Meredith had apparently not even taken off her jacket when attacked. And there is no indication independent of Guede that there was anything voluntary on Meredith's part in their encounter; his claims of consent seem typical of those of the apprehended rapist.
I propose, as others have concluded, that a burglary interrupted by Meredith's entry to the flat led to Guede deciding to attack and kill Meredith.