If they are particularly stubborn, wipe them down with vinegar to eat the deposits away.
If it's a matter of general spots after a wash, make sure you're not taking it into direct sun during/after washing. You can use some of the new super absorbent chamois or similar cloths to get better drying.
Had my wife's Pilot detailed recently, they used a professional water spot remover and rubbed lightly with AAAA steel wool. The remover was tan in color and consistancy of buttermilk. The remover came from a gallon can and was labeled "Water Spot Remover for Glass" not able to see the brand. Worked great, glass in clean and spot free.