I need to change the HTML structure of the E-Mail template for the "New Order E-Mail".
However I only see the tag {{layout handle="sales_email_order_items" order=$order}}
in the Template. How/where can I change what that tag generates?
Please check below file
app/design/frontend/default/your-theme/layout/sales.xml
And find below code
<sales_email_order_items>
<block type="sales/order_email_items" name="items" template="email/order/items.phtml">
<action method="addItemRender"><type>default</type><block>sales/order_email_items_order_default</block><template>email/order/items/order/default.phtml</template></action>
<action method="addItemRender"><type>grouped</type><block>sales/order_email_items_order_grouped</block><template>email/order/items/order/default.phtml</template></action>
<block type="sales/order_totals" name="order_totals" template="sales/order/totals.phtml">
...
...
</block>
</block>
</sales_email_order_items>
this code call this file
app/design/frontend/default/your-theme/template/email/order/items.phtml
if above file not fount in your theme then please check on base theme
app/design/frontend/base/default/template/email/order/items.phtml
Here you can change HTML structure if the email template