Copied from: https://apple.stackexchange.com/posts/98756
This can all be controlled by a Preference. Below is for Mountain Lion, which was changed slightly from Lion:
Apple Menu - System Preferences
General (under Personal section)
Select "Close Windows when quitting an Application" - this makes it so windows don't open when you reopen an app.
Now when you shut down (and tell it not to reopen windows on restart) they will not open then - or later.