Maybe allowing people to have control of the navigation menu so they can add or take away some navigation they want then to go in to each application and turn off or on what they want to see. Currently you get what you get and you can't do much about it with out doing some coding to change things. An interface to allow to do this may be a good idea.

Agreed, plus a sorting function for the links!

I hate to always do this hardcoded. This is something people want for vBulletin too, so be faster!

There is a script, Fusion Menu. You can find it in the marketplace. It does that perfectly, although i agree this functionality should be standard in invisionboard

Fusion menu (which is the menu here) does not allow users to add and remove their own links.

Whilst I agree with the OP, I would also like to see users given the choice of which items are shown in the sidebar - with certain items not being unselectable.