If you want to filter your product collection and want to show only in stock product than you can do as following.

You need to change in file Mage/Catalog/Model/Layer.php

Change the following function

public function prepareProductCollection($collection)
{
   $collection
         ->addAttributeToSelect(Mage::getSingleton('catalog/config')->getProductAttributes())
         ->addMinimalPrice()
         ->addFinalPrice()
         ->addTaxPercents()
         //->addStoreFilter()
         ->addUrlRewrite($this->getCurrentCategory()->getId());
        
    Mage::getSingleton('catalog/product_status')->addVisibleFilterToCollection($collection);
     Mage::getSingleton('catalog/product_visibility')->addVisibleInCatalogFilterToCollection($collection);
     return $this;
 }

To

public function prepareProductCollection($collection)
{
   $collection
         ->addAttributeToSelect(Mage::getSingleton('catalog/config')->getProductAttributes())
         ->addMinimalPrice()
         ->addFinalPrice()
         ->addTaxPercents()
         //->addStoreFilter()
         ->addUrlRewrite($this->getCurrentCategory()->getId());
        
Mage::getSingleton('catalog/product_status')->addVisibleFilterToCollection($collection);
     Mage::getSingleton('catalog/product_visibility')->addVisibleInCatalogFilterToCollection($collection);
     //return $this;
$collection->joinField(
       'stock_status',
       'cataloginventory/stock_status',
       'stock_status',
       'product_id=entity_id', array(
       'stock_status' => Mage_CatalogInventory_Model_Stock_Status::STATUS_IN_STOCK,
       'website_id' => Mage::app()->getWebsite()->getWebsiteId(),
      )
    );
   return $collection;
 }