How to prevent restoring all windows?

Ever since upgrading to Lion, every time I quit an app or shut down the computer, every window that was left open is automatically restored when I start that app up again or reboot the computer. How can I prevent this from happening, short of always closing every single window every time?
I believe that this has caused certain apps to freeze and quit upon start up.

Follow these instructions:
Launch System Preferences and click on the “General” icon
At the bottom of the “Number of recent items” list, uncheck the checkbox next to “Restore windows when quitting and re-opening apps”

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How to prevent restoring all windows?

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