/includes/classes/order.php around line 1003 you'll see:
Code:
$invoiceInfo=EMAIL_TEXT_INVOICE_URL . ' ' . zen_href_link(FILENAME_ACCOUNT_HISTORY_INFO, 'order_id=' . $zf_insert_id, 'SSL', false) . "\n\n"; $htmlInvoiceURL=EMAIL_TEXT_INVOICE_URL_CLICK;
$htmlInvoiceValue=zen_href_link(FILENAME_ACCOUNT_HISTORY_INFO, 'order_id=' . $zf_insert_id, 'SSL', false);
$email_order = EMAIL_TEXT_HEADER . EMAIL_TEXT_FROM . STORE_NAME . "\n\n" .
$this->customer['firstname'] . ' ' . $this->customer['lastname'] . "\n\n" .
EMAIL_THANKS_FOR_SHOPPING . "\n" . EMAIL_DETAILS_FOLLOW . "\n" .
EMAIL_SEPARATOR . "\n" .
EMAIL_TEXT_ORDER_NUMBER . ' ' . $zf_insert_id . "\n" .
EMAIL_TEXT_DATE_ORDERED . ' ' . strftime(DATE_FORMAT_LONG) . "\n" .
EMAIL_TEXT_INVOICE_URL . ' ' . zen_href_link(FILENAME_ACCOUNT_HISTORY_INFO, 'order_id=' . $zf_insert_id, 'SSL', false) . "\n\n";
To add the company name associated with the current customer, use $this->customer['company']