When you do a normal shutdown a dialog box will open you will see a check box next to the "Reopen windows when logging back in.". Un-check this. Now when your system boots up none of the extra open windows will be reopened. Only the programs in your start list will be opened.
The steps may be different for the specific OS level you are running and we have seen problems with this technique if you have OS 10.9 Mavericks.
Here is the link for a complete description of how to do this using a Terminal Command. https://discussions.apple.com/thread/3244852?start=30&tstart=0
The Terminal Command is Defaults write -g ApplePersistence -bool no
To reverse this use Defaults write -g ApplePersistence -bool yes