water spots are generally mineral deposits from drying water becoming more concentrated as it evaporates. Always make sure to chamois off the truck well, and if you want to you can wax the windows. If the spots wont come off there is a product called "Clay Magic" which works great for many things like rail dust, overspray, and hard water spots, it is quite expensive so you may want to see a detailer to see about doing it for you. Possibly a neat freak such as yourself (me too) could justify buying it.
Beware the newspaper idea for the inside. Some folks say that drying a cleaned window with newspaper adds shine to the glass. They're right, but you don't want to do that on the inside of the glass. Otherwise, you'll be screwed the next time you drive into the sun.
...and yes, like everything else, I learned this the hard way.