One of the easiest and safest ways to shut down all of your running
programs so that you can do a defrag, a scandisk, or whatever is to use a
program called Enditall.  

Just install end it all and the scripts and execute it.  When you go into
the program after installing it you'll probably have to shift-tab once to get to
the list of your running programs.  Enditall will already protect the programs
such as the system tray that are necessary for your computer to function, and
the only other thing that I suggest protecting is your screen reader.  You
protect a program by hitting your spacebar or pressing alt + P while highlighted
on it.  After you have the programs protected that you don't want to shut
down just tab to the Enditall button and hit enter.  That will close all of
the running programs that aren't protected and then you need to tab to exit
and hit enter.  End it all will remember the programs you have protected for the
next time.

Now you can defrag your drive, run scandisk, or whatever you want to do and
after you finish that, just rebooting the computer will restart the programs
that Enditall shut down.