I'm using an Arduino Ethernet shield and a prototype shield wih an Uno.
At the moment, prototype shield is just supplying 7.5V to the Vin connector and using pin 9 for pwm output. All the other pins just connect through.
If I put the ethernet shieild on the arduino and then the prototype shield on top, all works ok but if I swap the ethernet and prototype shield, the ethernet shield doesn't work.
The only difference I can see is that the ICSP connector is not connected when the ethernet shield is on top but I understood that these lines are duplicated on pins 11, 12 and13 which are connected through.
I prefer to put the ethernet sheild on top because of the height of the rj45 connector height.