I freeze mine all the time... no problems! You don't leave them for days... just 10-15 minutes.
As for the butter vs margarine vs shortening... margarine will definately give you cookies that spread more as it contains more water that butter or shortening. Unless your recipes specifically says butter or margarine, stick to butter (and margarine does not mean the soft spread stuff... it has even MORE water in it!
Whenever I make choco chip cookies, I always double the recipe and freeze the extra dough... just roll it into a sausage shape (diameter about the same as you'd want a cookie) in a sheet of waxed paper... twist the ends and pop it in the freezer! Then I can make just a couple of cookies... I just cut off (with a sharp, hot knife) individual cookie amounts... plop them on a cookie sheet, and bake 'em up!
BTW... if you're making a big batch of cookies and re-using your cookie sheets, make sure they are cooled before adding the next batch of dough or you'll have the same spread problems.