Magento – How to send diffrent order emails to admin and customer

I don't have a working code for this, but here is an idea.
You can try to rewrite the Mage_Sales_Model_Order::sendNewOrderEmail() method and use different templates depending on the products ordered.

The section in charge of determining the mail template to use is this:

    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();
    }

You can change this in order to depend on the products.

To get the products ordered you can use in the function above:

$items = $this->getAllItems();
foreach ($items as $item) {
    $itemSku = $item->getSku();
    $product = $item->getProduct();
}

You can create product attribute where you can specify what template to be used then you can decide based on that. Of course you will need to specify a priority in case 2 products are ordered so you will know what template to use. But you better your logic.

There are two separate sections that handle the Magento emails:

1. Store Email Addresses define addresses for senders of mails sent by the system. (General, Sales, Support)

2. Sales Emails define which emails are sent and by which sender (as well as sending a copy to an admin if you would like to receive one).

3. System->Configuration->General->Store Email Addresses are only the sender addresses that will appear in the emails sent. These fields have nothing to do with admins receiving emails or order notifications. It's just a place to define sender email/return address for the system to use in the header. General Sales, Sales Representative, Support, etc.

4. System->Configuration->Sales->Sales Emails is where you configure which of the Store Email addresses you specified in the Store Email Addresses section will be the sender of New Orders, Comments, Invoices, etc. By default, customers receive new order emails from the Sales Representative email address defined under Store Email Addresses

Sales Emails is where you configure the system to send a copy of an order to you as the admin, under (Send Order Email Copy To:)