Well, it depends. :^)

If this is an HTML-related question, then I've always preferred to use a LoL along the following lines:

• my @submenu = ('div', 'img', 'alt');
• my @menu = (
  • ('div', 'img', 'alt', \@submenu)
• );

This does away with the sorting issue and gives you a fairly obvious way to change parameters in a menu so that if you need a special icon or want to manipulate the menu while writing an HTML file, you can.

Of course, this doesn't have any obvious mechanism for drawing your nodes correctly (this straight scenario works best for DHTML menus where elements aren't supposed to cause a reflow.

For displaying a tree more properly I've found JavaScript objects to be pretty handy (unless you want to write for NN3 or IE3 and early IE4) -- you create a Tree object and Node object and then assign your nodes to the tree in any order using some kind of simple path system. Each node 'knows' how deep it is in the tree (since it can query its parent node) and can draw itself appropriately (again, by querying its parents as necessary).

I don't know if this exactly answers your question since it's unclear (to me at least) what your output format is, and I do like some aspects of your system a lot (the matrix transformations seem quite quick and simple), while having doubts about others (the numbering scheme is unduly difficult for a human to read).

HTH