Practically every place you might submit a story to will include its formatting guidelines, and they almost always stress (furiously) that you have to adhere to it. Rightly so. In many cases, however, they simply specify ‘standard manuscript format’.
So, here is a link to a wonderful example of standard manuscript format for a short story. If you want to go straight to the Microsoft Word template file, it can be found here.
The same site also provides a proper formatting guide for novels, too.
Tris Matthews 
The first time I’ve seen any reference to a short story manuscript format other than the Shunn one, though it is very similar: http://www.sfwa.org/2008/11/manuscript-preparation/
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