I've come to think it's not the window causing it, despite how exerting pressure on the window stops or reduces the noise. I think its more to do with the seals at the top rearmost part of the door, as the noise is present even with the window down. When I notice the noise, I can see a lot of flexing between the door and the body. If I jam my finger into the gap between the door and the frame at the top, the noise also goes away. So I think it's the plastic seals at the top rear part of the door. However, no amount of cleaning or lubrication seems to help. I should be visiting the dealer soon, so I'll let you know if they've got a solution, I reckon a minute adjustment of the door latch might solve the problem.,
As for general creaking from the top, despite living in a cobblestoned area, I don't hear any creaks or rattles from the top, or from anywhere else for that matter. The only noise is this door/window clicking behind my right ear and it's driving me nuts.