Magento – Logos in transactional emails are different

Use the google url builder get a good campaign url: https://support.google.com/analytics/answer/1033867?hl=en

It will take your base url and create a tracking url based on your info that you add and presents a link like: http://www.savethemage.com/?utm_source=Newsletter&utm_medium=Email&utm_content=Logo&utm_campaign=Order+Confirmation

Then take the part starting with ?: ?utm_source=Newsletter&utm_medium=Email&utm_content=Logo&utm_campaign=Order+Confirmation

and add it to the transaction email template for each link you want to track. Make sure you change the utm_content= to something unique for each link.

Then analytics will track all of those clicks.

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.