Mage::log('Start');
 
// Set indexing to manual before starting updates, otherwise it'll continually get slower as you update
$processes = Mage::getSingleton('index/indexer')->getProcessesCollection();
$processes->walk('setMode', array(Mage_Index_Model_Process::MODE_MANUAL));
$processes->walk('save');
 
/** @var Varien_Db_Adapter_Pdo_Mysql **/
$dbw = Mage::getSingleton('core/resource')->getConnection('core_write');
$productCategoryTable = Mage::getSingleton('core/resource')->getTableName('catalog/category_product');
 
$product_ids = Mage::getModel('catalog/product')->getCollection()
    ->getAllIds();
 
$category_id = 123;
 
// Add product ids and category ids to database for insertion
$data = array();
foreach($product_ids as $id) {
    $data[] = array(
        'category_id' => (int)$category_id,
        'product_id'  => (int)$id,
        'position'    => 1,
    );
}
 
if(count($data)) {
    // Updates a single attribute, much faster than calling a full product save
    try {
        $dbw->insertMultiple($productCategoryTable, $data);
    } catch (Exception $e) {
        //ignore duplicate entry error messages
        if(strpos(strtolower($e->getMessage()), 'duplicate entry') === FALSE) {
            Mage::log($e->getMessage());
        }
    }
}
Mage::log('Products Put in Category:');
Mage::log($product_ids);
 
 
// Reindex all
$processes->walk('reindexAll');
// Set indexing back to realtime, if you have it set to manual normally you can comment this line out
$processes->walk('setMode', array(Mage_Index_Model_Process::MODE_REAL_TIME));
$processes->walk('save');
 
Mage::log('End');