Use discreet/simple animated features to create seamless transitions from one section the the other. This helps the user to create a mental map of navigation/structure.
Use short (one word if possible) titles on the buttons that describe clearly the essence of the action.
Use semantic zooming where possible (a good example is how zooming works on Google/Bing maps, where more information is visible when you focus on an area).
Create at least two ways to navigate: Vertical and horizontal. Vertical when you navigate between different sections and horizontal when you navigate within the contents of the section or subsection.
Always keep the main options nodes of your structure visible (where the size of the screen and the type of device allows it).
When you go deep into the structure always keep a visible hint (i.e. such as in the form of a path) indicating where you are.
Hide elements when you want the user to focus on data (such as reading an article or viewing a project). - however beware of point #5 and #4.
