how tall do you make your walls for structures?

How big are the walls in your house?  Add a foot for floor joists. There's 1 level. Double that for the next level, etc. Top off with another foot for final floor.  Some building are bigger/smaller than others.  Gauge that based on doors and window sizes.

Are we talking houses or industrial or Main Street small town or large city buildings or ?

Story height for larger buildings averages between 13 and 14 feet.  

I use OGR Ameri-Towne buildings as a reference. Each wall is 3 inch or 12 scale feet.