i'm no aerodynamicist (sp?) but the roof seems like the best place if you want air in the cabin.
let me explain my reasoning:
there is alot of airflow over the roof of the car, in fact the air sticks to the downward slope of the roofline towards the hatch (creating lift). This would give you alot of air going into the car. Compared to the high pressure air accumulation by the bottom of the windshield, it seems that the roof would give you more velocity, and more pressure with the air coming in, than say, the stock fresh air vents on my 280z, which would almost be the same as putting the intakes on the inspection lids.
I wouldn't do functional "ealonor" style quarter window intakes, because when you open you windows you get lower cabin pressures, so it seems that putting the vents that close to the windows would maybe not be as effective in getting air into the cabin as the roof scoop.