When switching from DSO to SUPHP in cpanel (a must for anyone who takes security seriously on a public webserver), one must pay careful attention to the insecure permissions of user’s public_html folders. The following commands will look in every user’s html folder and make the appropriate CHMOD to allow php to properly execute under SUPHP. Don’t forget to also check for files owned by ‘nobody’ or ‘root’ — they will also fail with a 500 error.
find /home/*/public_html/ -type d -print0 | xargs -0 chmod 0755 # For directories
find /home/*/public_html/ -type f -not -name "*.pl" -not -name "*.cgi" -not -name "*.sh" -print0 | xargs -0 chmod 0644 # For files
find /home/*/public_html/ -type f -name "*.cgi" -print0 -o -name "*.pl" -print0 -o -name "*.sh" -print0 | xargs -0 chmod 0755 # For CGI/Scripts 