Are you trying to run these apps via a web server? If so, do you have them in the specified directory for apache to run cgi-scripts? I am not sure where debian installs apache, but if it is in something line /usr/local/apache you should see a directory in there titled cgi-bin. Put your cgi scripts in there.
To learn more about where these directories are or to add more, less through the httpd.conf file. You will have to restart apache if you make any changes.