5 door for me for the practicality, as we regularly take our dog in the back of the car (shock horror), and he likes to have the rear window cracked down a little to give a bit of air flow and cool him down, something I've been unable to do for the last 2½ years in the Scirocco. Plus, I'm in the minority and actually prefer the looks of the 5 door to the 3 door.
As has been mentioned as well (and have a Scirocco know this well), the 3 door cars have huge doors which are not only heavy, but restrict getting in and out when parked in car parks etc.