Option one: use a skin-specific or shared menu, parsed with the generic menu parser included in some skins, to output a site-configured header-specific menu.

(See Splash, HasSomeColours, others as an example, where those use the global-links-menu message)

Option two: make dropdowns of standard menus: Sidebar, toolbox, languages, user links; only show sidebar in particular as such on resolutions where the full sidebar cannot be rendered