If you are using OS X Mountain Lion, when you are going to turn off the Mac, untick "Reopen windows when logging back in", so opened applications won't start up automatically the next time you turn on the Mac.
If it doesn't work, open System Preferences > Users and Groups > Login Items, and delete the apps you don't want
"Reopen windows..." was already unchecked, and there's something wrong with System Preferences that make that fix unworkable. It may be beyond the scope of this site to fix it. The problem with System Preferences is that as soon as I place a checkmark for one of the applications, the spinning ball appears and doesn't go away. I have tried restarting the computer several times, and now I'm going to use Disc Utiity. Whenever I've had problems iike this in the past, the remedy was usually to fix a corrupted preference by dragging it to the trash and restarting the computer; however, I always did that while being guided by an expert. I wouldn't want to risk messing things up by doing it by myself. I have used "Force Quit" to clear the deck, but that didn't help.