Hi
The noise sounds like  pre ignition 
Solutions here 
http://yarchive.net/car/knock.html
I've never heard of a brake servo knocking - are you sure you mean the servo?
Sounds like the rear subframe bushes are worn (assuming it's a hatchback - the estate does not have them) these can now be replaced without replacing the whole subframe - don't let anyone tell you differently  - difficult to diagnose without seeing the car
There's a good Mondeo forum here 
http://www.fordmondeo.org/forum/fusionbb.php?
                
 Fiesata
                
 June 2009