I have a black R33 - dark coloured cars show water stains and residue a lot more than lighter coloured cars.
I find that washing the car in sections and rinsing helps prevent the stains appearing (ie: wash roof and windows - rinse car, wash mid section - rinse car, wash lower section - rinse car). Also the sooner you can get the water off the car with a chamois after washing, the better
If you've still got marks, you could try using Meguiars Quick/Speed Detailer on a cloth and give the car a wipe over...