I was just yesterday comparing the codebase used in current NavMenu in WP 3.0 with WooMenus, and I couldn't find anything that these two share. WooMenus can't be expanded, they support only link, page and category for menu items, all data is stored in sepparate tables in DB. WooThemes really did come up with excellent concept for the menus, and up to a Beta 2 release of WP 3.0, I preferred Woo implementation, because WP version was constantly broken and causing problems.

But, with WP version there are some things I really don't like: use of taxonomies for menu items. I would prefer if the menus are stored as serialized objects, most operations would be much faster that way. Also, I find strange the decision to put items widgets to the left instead of right as we all used to with other WP panels.