Hi Magento have setuped simple and configurable product relation on catalog_product_super_link.

So.You need filter product COllection by this product ids

Step1: Get list of all simple product which is used config product child product 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();

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();     

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();

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.

Hi Magento is simple and configurable product relation on catalog_product_super_link.

So.You need filter product COllection by this product ids

Step1: Get list of all simple product which is used config product child product byusing belowc ode

$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();

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();     

Hi Magento have setuped simple and configurable product relation on catalog_product_super_link.

So.You need filter product COllection by this product ids

Step1: Get list of all simple product which is used config product child product 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();

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();