Menu Plug Ins

I have looked for plug-ins for drop down menus, mega menus and floating menus on WPMU Dev.... Nothing out there that I can find.

On there are many plug-ins for those functions, several done by Remix4. Most use Jquery. Only one was listed as a Multisite plug-in (custom-taxonomies-menu-midget).

My questions are:

How will plug-ins for menu capabilities integrate in a multisite environment? What is the downside? Any suggestions for multiple drop down style menus in the header?