<global>
    <template>
          <email>
                 <custom_email_template>
                     <label>My Label</label>
                     <file>myfile.html</file>
                     <type>html</type>
                  </custom_email_template>
          </email>
    </template>
</global>

$emailTemplate  =  Mage::getModel('core/email_template')->loadDefault('custom_email_template');

$emailTemplate  =  Mage::getModel('core/email_template')->loadByCode('custom_email_template');

$processedTemplate = $emailTemplate->getProcessedTemplate($emailTemplateVariables);