I've been noticing a ton of this error in my server log.
Timeout waiting for output from CGI script /home/.../public_html/mydomain/index.php
*this is a multi-domain installation
I've got about 80 instances of this error today alone. It seems to be coming from the same few IP addresses as well.
You should contact your hosting provider for this issue. (Magento doesn't use CGI on it's own)