<global>
    <models>
        <sales>
            <rewrite>
                <order>MyModuleNameSpace_Mymodules_Model_Sales_Order</order>
            </rewrite>
        </sales>
    </models>
</global>

// Retrieve corresponding email template id and customer name
        if ($this->getCustomerIsGuest()) {
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
            $customerName = $this->getBillingAddress()->getName();
        } else {
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
            $customerName = $this->getCustomerName();
        }

<?php
class MyModuleNameSpace_Mymodules_Sales_Order extends Mage_Sales_Model_order
{
    const XML_PATH_EMAI_SPECIAL_TEMPLATE         = 'sales_email/order/special_template';


    public function queueNewOrderEmail($forceMode = false)
    {
        ......
        /* add this code */
        $items =$this-->getAllItems();
        $match=false;
        foreach ($items as $itemId => $item)
        {
            if( $item->getSku()=='YOUR_SPECIAL_PRODUCT'){
            $match=true;
            }

        }


        // Retrieve corresponding email template id and customer name
        /* this conditions */
        if($match){
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAI_SPECIAL_TEMPLATE, $storeId);
            $customerName = $this->getBillingAddress()->getName();

        }
        elseif($this->getCustomerIsGuest()) {
            /* change if to else if  */
        //if ($this->getCustomerIsGuest()) {
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_GUEST_TEMPLATE, $storeId);
            $customerName = $this->getBillingAddress()->getName();
        } else {
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAIL_TEMPLATE, $storeId);
            $customerName = $this->getCustomerName();
        }

    ....

        return $this;
    }



}

if($match){
            $templateId = Mage::getStoreConfig(self::XML_PATH_EMAI_SPECIAL_TEMPLATE, $storeId);
            $customerName = $this->getBillingAddress()->getName();

        }