Uncanny. I posted a very similar question on the Ford Focus General Dicussion board today. I too have exactly the same creak.Purchased my 56 1.8 zetec just a week ago. Quiet as a mouse on the road, but take it around the side streets, and over road humps and somewhere around the rear doors is a creak.
I also thought it might be the door seals rubbing together, i.e. the one on the door rubbing agains the one on the door frame as the car flexes. Word of warning - don't use vaseline or any products like it. They all attack rubber, and will ruin your seals. I am going to try spraying my seals with Silicon spray - you can get it from Halfords. It looks and works like a lubricant, but doesn't harm the rubber.
I am a but peaved though. I had a 1994 Passat for 10 years, and it never creaked once. I would have thought that the body rigidity of the C1 Focus platform would be up there with the best, particularly as it's handling is well regarded. My car has only done 18k miles too! I dread to think what it would sound like if it reaches 130k miles like my old Passat!!!
The rear parcel shelf tends to clatter about over rough roads too. I think you notice it more because the car is quite hushed otherwise.