[eluser]Rick Jolly[/eluser]
There are tons of things you can do. I'd start by putting the logic for the navigation in a library, and returning the navigation partial view as a string from that library. Then you could:
1) assign the partial view as a variable in each of your controller contstructors using $this->load->vars();
2) create an application/base/parent controller and do the same thing as in #1, but you'd only have to do it once.
3) create a helper that calls your library directly from the main layout view, so you wouldn't have to touch the controllers. For an example, search for hmvc on these forums.