Magento has simple and configurable product relation in `catalog_product_super_link` table. So you can use advantage from this table.

Basically what you have to do is, ***filter the simple product collection by the product ids present in `catalog_product_super_link` table***


**Step1:** Get list of all simple products by using below code

    $collectionSimple = Mage::getResourceModel('catalog/product_collection')
        ->addAttributeToFilter('type_id', array('eq' => 'simple'));
    				
    $collectionSimple ->getSelect()->join(array(
        'link_table' => 'catalog_product_super_link'),
        'link_table.product_id = e.entity_id',
        array('product_id')
    ));

    $IdsSimpleCon=$collectionSimple->getAllIds();

![enter image description here][1]

**Step2:** Make another product Collection exclude of step one product collection and code 


    $NonConfigurablecollectionSimple = Mage::getResourceModel('catalog/product_collection')
        ->addAttributeToFilter('type_id', array('eq' => 'simple'))
        ->addAttributeToFilter('entity_id',array('nin'=>$cond ));
    		
    echo $NonConfigurablecollectionSimple->getSelect();	

Now, `$NonConfigurablecollectionSimple` would hold all those simple product which does not have a single relationship with configurable products.	


  [1]: https://i.sstatic.net/277v4.png