It's so annoying. You go to shutdown or restart your PC and you walk away, expecting your computer to be powered off (or rebooted) by the time you come back. You go to the fridge, grab a drink and return to find a message on your screen that says you have apps which aren't closed.
Maybe you just had a nearly-empty notepad doc or a picture in Photoshop that you didn't want to save because you already copied and pasted the data into another app. Now, Windows is nagging you to go back and close all your apps manually. Yes, Windows gives you a button that says "Shut down anyway," but you have to hit it and wait for the system to hopefully force close the apps.
The best solution is to open the registry editor, navigate to \HKEY_CURRENT_USER\Control Panel\Desktop and create three strings (if they don't already exist). Create AutoEndTasks and set it to 1, create WaitToKillAppTimeOut and set it to 2000. Finally, create HungAppTimeOut and set that to 2000 also.