Actually, for a graphics card those pads might be better, yeah. At least to avoid something not making contact. I did replace the pad for the GPU with grease on my 8800; shaved off some 5C in idle, probably more under load.
My point about the Intel cooler is that it creates turbulence. Air is forced down and out in all directions as it is forced out the sink. A good portion of the hot air trying to move towards those exhaust fans will get drawn into the cooler again. If you can get a small tower-design in there, you can have the air move through more cleanly, straight towards exhaust fans.
Anyway, good luck with the new case.
