Change sort order of Magento subcategories

Try calling getChildrenCategories this will take into account the position of each category:


$loadCategory->getChildrenCategories()
EDITED



Unlike getChildren which returns a string of all category ids returns
 an array of Mage_Catalog_Model_Category so your code will need to be 
changed to take this into account.



From your code snippet above the following change should work. Note 
the call to getChildrenCategories() and the change in the foreach loop 
as each item should be a category object.

<?php
$currentCat = Mage::registry('current_category');

if ( $currentCat->getParentId() == Mage::app()->getStore()->getRootCategoryId() )
{
    // current category is a toplevel category
    $loadCategory = $currentCat;
}
else
{
    // current category is a sub-(or subsub-, etc...)category of a toplevel category
    // load the parent category of the current category
    $loadCategory = Mage::getModel('catalog/category')->load($currentCat->getParentId());
}
$subCategories = $loadCategory->getChildrenCategories();

foreach ( $subCategories as $subCategory )
{
    if($subCategory->getIsActive())
    {
        echo '<a href="'.$subCategory->getURL().'">'.$subCategory->getName().'</a>';
    }
}
?>