Magento – How to add layered Navigation filter as stock availability

Best place to add filters to product collection programmatically is

Mage_Catalog_Model_Layer::prepareProductCollection()

not phtml template.

At the moment catalog/product/list.phtml is rendered, product collection is already loaded and if you don't plan to render products it is better not to load them at all.

The logic should sound like:

public function prepareProductCollection($collection)
{
    $collection
        ->addAttributeToSelect(Mage::getSingleton('catalog/config')->getProductAttributes())
        ->addMinimalPrice()
        ->addFinalPrice()
        ->addTaxPercents()
        ->addUrlRewrite($this->getCurrentCategory()->getId());

    Mage::getSingleton('catalog/product_status')->addVisibleFilterToCollection($collection);
    Mage::getSingleton('catalog/product_visibility')->addVisibleInCatalogFilterToCollection($collection);

    // your custom filter
    if ($this->_areFiltersApplied()) {
        $this->_addInStockFilter($collection);
    }

    return $this;
}

protected function _areFiltersApplied() {
    return count($this->getState()->getFilters()) > 0;
}

protected function _addInStockFilter($collection) {
    Mage::getModel('cataloginventory/stock_status')->addIsInStockFilterToCollection($collection);
}

Layered navigation filters are rendered in catalog/layer/view.phtml template:

            <?php foreach ($_filters as $_filter): ?>
            <?php if($_filter->getItemsCount()): ?>
                <dt><?php echo $this->__($_filter->getName()) ?></dt>
                <dd><?php echo $_filter->getHtml() ?></dd>
            <?php endif; ?>

Here you can add checks for category and attribute id (replace the code aabove with the code below):

            <?php 
                $_categoryId = $this->getLayer()->getCurrentCategory()->getId();
                $_categoryFilters = array(
                    // top level categories
                    array(
                        'categories' => array(5,8,10),
                        'attributes' => array('color', 'size'),
                    ),
                    // second level categories 
                    array(
                        'categories' => array(6, 7, 9, 11),
                        'attributes' => array('manufacturer'),
                    ),
                );
            ?>
            <?php foreach ($_filters as $_filter): ?>
            <?php 
                $_found = false;
                foreach ($_categoryFilters as $_categoryFilter) {
                    if (in_array($_categoryId, $_categoryFilter['categories']) &&
                        (!($_attribute = $_filter->getAttributeModel()) ||
                        in_array($_attribute->getAttributeCode(), $_categoryFilter['attributes']))
                    )
                    {
                        $_found = true;
                        break;
                    }
                }
            ?>
            <?php if($_found && $_filter->getItemsCount()): ?>
                <dt><?php echo $this->__($_filter->getName()) ?></dt>
                <dd><?php echo $_filter->getHtml() ?></dd>
            <?php endif; ?>