The quite new menu system where you can build arbitrary menus is a big step an a great direction. I am missing one thing, though: menu items that link to tags, that is a list of posts being tagged appropriately, and pseudo items, that is items without a link.
|- Project A (page)
| |- Demo (page)
| |- FAQ (page)
| |- Blog (posts tagged 'project-a')
|- Project B (page)
|- Old Projects (pseudo)
| |- Old Project A (page)
| |- Old Project B (page)
|- Ideas (posts tagged 'idea' and 'projects')
Of course, combination of tags should be natively supported. I would like to have separate menu items for book+computer-science and book+spare-time.
This can be done by custom link items but I think WordPress should give a nice frontend for handling its own categorisation means. In particular, the new mechanism should be robust against tag renaming (which a custom link is not).
Pseudo items should be there just to give an easy and lightweight way to create sophisticated menu structures.
You can even go further and identify posts and pages, that is allow menu items that link to a single, specific post (as possible for pages) and allow pages to be categorized and tagged (which could make them pop up on category/tag based searches).