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();