D7: Create an administration page for my module
First of all hook_mail_alter() only has 1 parameter, no $form_state. Second of all, the system_settings_form() will save the form values into the variables table in the database. To access that value you should use variable_get().

Now, your code should look like this:

// try to change body to something more specific to your module, like custom_email_body
$form['mail_template']['custom_email_body'] = array( 
  '#type' =&gt; 'textarea',
  '#title'  =&gt; t('Email template'),
  '#default_value' =&gt; variable_get('custom_email_body', ''),
  '#rows' =&gt; 10,  
);


then:

function shop_mail_alter(&amp;$message) {
$client_body = variable_get('custom_email_body', '');
if (is_array($message['body'])) {
    $message['body'][] .= $client_body;
  }
}