Hi
you can add customer company in new order email by adding the template variable in modules/mailalerts/mailalerts.php.
Add
$template_vars['{customer_company}'] = $customer->company;
below where $template_vars array is defined in hookActionValidateOrder function of modules/mailalerts/mailalerts.php.
so the code look like
$template_vars = array(
'{firstname}' => $customer->firstname,
'{lastname}' => $customer->lastname,
'{email}' => $customer->email,
'{delivery_block_txt}' => MailAlert::getFormatedAddress($delivery, "\n"),
'{invoice_block_txt}' => MailAlert::getFormatedAddress($invoice, "\n"),
'{delivery_block_html}' => MailAlert::getFormatedAddress($delivery, '<br />', array(
'firstname' => '<span style="color:'.$configuration['PS_MAIL_COLOR'].'; font-weight:bold;">%s</span>',
'lastname' => '<span style="color:'.$configuration['PS_MAIL_COLOR'].'; font-weight:bold;">%s</span>')),
'{invoice_block_html}' => MailAlert::getFormatedAddress($invoice, '<br />', array(
'firstname' => '<span style="color:'.$configuration['PS_MAIL_COLOR'].' font-weight:bold;">%s</span>',
'lastname' => '<span style="color:'.$configuration['PS_MAIL_COLOR'].'; font-weight:bold;">%s</span>')),
'{delivery_company}' => $delivery->company,
'{delivery_firstname}' => $delivery->firstname,
'{delivery_lastname}' => $delivery->lastname,
'{delivery_address1}' => $delivery->address1,
'{delivery_address2}' => $delivery->address2,
'{delivery_city}' => $delivery->city,
'{delivery_postal_code}' => $delivery->postcode,
'{delivery_country}' => $delivery->country,
'{delivery_state}' => $delivery->id_state ? $delivery_state->name : '',
'{delivery_phone}' => $delivery->phone ? $delivery->phone : $delivery->phone_mobile,
'{delivery_other}' => $delivery->other,
'{invoice_company}' => $invoice->company,
'{invoice_firstname}' => $invoice->firstname,
'{invoice_lastname}' => $invoice->lastname,
'{invoice_address2}' => $invoice->address2,
'{invoice_address1}' => $invoice->address1,
'{invoice_city}' => $invoice->city,
'{invoice_postal_code}' => $invoice->postcode,
'{invoice_country}' => $invoice->country,
'{invoice_state}' => $invoice->id_state ? $invoice_state->name : '',
'{invoice_phone}' => $invoice->phone ? $invoice->phone : $invoice->phone_mobile,
'{invoice_other}' => $invoice->other,
'{order_name}' => $order->reference,
'{shop_name}' => $configuration['PS_SHOP_NAME'],
'{date}' => $order_date_text,
'{carrier}' => (($carrier->name == '0') ? $configuration['PS_SHOP_NAME'] : $carrier->name),
'{payment}' => Tools::substr($order->payment, 0, 32),
'{items}' => $items_table,
'{total_paid}' => Tools::displayPrice($order->total_paid, $currency),
'{total_products}' => Tools::displayPrice($order->getTotalProductsWithTaxes(), $currency),
'{total_discounts}' => Tools::displayPrice($order->total_discounts, $currency),
'{total_shipping}' => Tools::displayPrice($order->total_shipping, $currency),
'{total_tax_paid}' => Tools::displayPrice(($order->total_products_wt - $order->total_products) + ($order->total_shipping_tax_incl - $order->total_shipping_tax_excl), $currency, false),
'{total_wrapping}' => Tools::displayPrice($order->total_wrapping, $currency),
'{currency}' => $currency->sign,
'{message}' => $message
);
$template_vars['{customer_company}'] = $customer->company;
and use {customer_company} in new_order email template where you want to display the customer company.