We always used whink at toyota. It takes off water spots on paint and windows. You just can't do a windshield with it.
http://www.whink.com/rust_stain_remover.htm
You have to use it in the shade. I always use a cloth wax applicator to rud it in in small 12x12 areas. Don't let it get dry. You rud it in circular motions for about 15-20 seconds then spray it with windex. wipe clean with a rag and spray with windex one more time to clean it off. The water spots disappear. Try it, you wont be dissapointed. Just don't use it on the windshield. They sell it at walmart.