Here's an interesting thing about the broken window:
In Hendry's analysis of the way in which the window was broken, he makes the insightful observation that the condition in which the window was found is incompatible with a single impact from a blunt object. In windows of this sort, the pane is held in position round the edges with tack nails and putty. This essentially adheres the glass to the frame all around the edge.
Consequently, when such a window is hit with a blunt object (e.g. a rock), the glass will break around the point of impact, but will typically remain in place around the edges, owing to the adhesion between the glass and the frame. However, in the case of Filomena's broken window, there is very little glass in place around the frame in the entire lower half of the window.
This therefore strongly implies that glass was manually removed (either pulled out or snapped off) all around the frame, after the initial rock impact. This is itself entirely consistent with an actual entry through this window, since the intruder would need to put his arm through the broken window to reach the latch, and it would therefore be logical for him to remove any jagged pieces of glass around the edges to avoid cuts or catching his clothing.
However, the obvious question is whether two scared, stoned stagers (ooh, I've caught Stint's alliteration bug!) would be so aware as to think through the staging to the extent that they removed the glass round the edges of the window? To me, it would take a significant amount of thought on behalf of potential stagers to realise that an actual intruder would have likely needed to perform this step. Given that we can assume that neither Knox nor Sollecito had any real-word experience of breaking and entering, I find it hard to see how this level of detail would have come to mind to them if they had indeed staged the break-in...