Need to get the Product categories output for custom scripts (like I am doing).  Here is a basic prototype to begin:

// Nevermind - this will not make subcats, the children are all from the main
$obj = new Mage_Catalog_Block_Navigation();
$store_cats    = $obj->getStoreCategories();
$current_cat     = $obj->getCurrentCategory();
$current_cat    = (is_object($current_cat) ? $current_cat->getName() : '');

foreach ($store_cats as $cat) {
  echo '1- '.$obj->getCategoryUrl($cat).' 2- '.$cat->getName().' - -';
  foreach ($obj->getCurrentChildCategories() as $subcat) {
    echo 'A- '.$this->getCategoryUrl($subcat).' B- '.$subcat->getName();
  }
}

// author : @marwei / datamafia.com / interzonemultimedia.com
// Check this out! for one level deep cat menu that you can place anywhere

// get your object
$navobj = new Mage_Catalog_Block_Navigation();
$store_cats    = $navobj->getStoreCategories();

// open the list
$ret = '<ul id="corpDesMageNav">';
// parent cat loop
foreach ($store_cats as $cat) {
 $ret .= '<li>'.$cat->getRequestPath().' - '.$cat->getName().'</li>';
 $subcats = $cat->getChildren();
 // one deep subcategory
 $subCtr = 0; // for counting in the next foreach
 $closeUL = false;
 // reset the trigger // Child cat / one deep loop
 foreach($subcats as $kid){
 if ($subCtr==0) { // first itteration opens the (nested) <ul>
 $ret .= '<ul style="margin-left:20px;"><!-- Only a helper for the subcat -->';
 $closeUL = true;
 }
 $subCtr++;
 $ret .= '<li> [sub cat] '.$kid->getRequestPath().' + '.$kid->getName().'</li>';
 }
 if ($closeUL == true) { // close the ul based on event trigger
 $ret .= '</ul>';
 }
}
$ret .= '</ul>';
echo $ret;

Notes on the (revised) above content. Most (but not all???) of the methods from the Class work (Magento reference).  The above example provides you with the big pieces of information. The Cat Name and the Cat Link.

More importantly – this method allows you to use the menu system ANYWHERE! You are not working with $this->stuff, instead you are dropping isolated instances. My need arised because we are switching in important legacy information and programs in the middle of Magento.   Trust me when I say No ecommerce software was ready for what we are doing.

So I can drop in custom scripting in the content pane using a simple content controller and variable sniffer inside the Magento system and then drop menus and such with out head ache.

The example is FAR from your final output, but this is enough for a programmer with medium skill to get a custom navigation going.  My output has some “garbage” in there to help look at the category information. It should only take a minute to clean it up and check Strict.

And, as a friendly reminder, watch your “default category”.  Magento (at the time of this post) reads from the top level category, no exceptions.  There is plenty of documentation on this topic in the forums.

I hope this helps, let me know if you need more!

/*
 ONE FINAL EXAMPLE - 3 levels deep!!!!
 If anyone wants to write this into a fully recursive function/class let me know. I only need 3 deep
Adding another nested foreach is easier than a unit test on recursion.
*/

// get your object
$navobj = new Mage_Catalog_Block_Navigation();
$store_cats    = $navobj->getStoreCategories();

// open the list
$ret = '<ul id="corpDesMageNav">';
foreach ($store_cats as $cat) {
 $ret .= '<li>'.$cat->getRequestPath().' - '.$cat->getName().'</li>';
 $subcats = $cat->getChildren();
 // one deep subcategory
 $subCtr = 0; // for counting in the next foreach
 $closeUL = false;
 foreach($subcats as $kid){
 if ($subCtr==0) { // first itteration opens the (nested) <ul>
  $ret .= '<ul>';
  $closeUL = true;
 }
 $subCtr++;
 $ret .= '<li style="margin-left:10px;"> [sub cat] '.$kid->getRequestPath().' + '.$kid->getName().'</li>';
 // ome more deep - we got children?
 $subSubCtr = 0;
 $closeSubUL = false;
 if($kid->hasChildren()==1){
  $subSubCat = $kid->getChildren();
  foreach($subSubCat as $grandKid){
   if ($subSubCtr==0) { // itteration opens the (nested) <ul>
   $ret .= '<ul>';
   $closeSubUL = true;
  }         
  $ret .= '<li style="margin-left:20px;"> [sub sub cat] '.$grandKid->getRequestPath().' + '.$grandKid->getName().'</li>';
 }
 if ($closeSubUL == true) { // close the ul based on event trigger
  $ret .= '</ul>';
 }
}
}
 if ($closeUL == true) { // close the ul based on event trigger
 $ret .= '</ul>';
 }
}
$ret .= '</ul>';
echo $ret;