Matt,
Have you thought about giving this tool a bit of an overhaul? It's long overdue one you know!
I love the navigation toolbar, but the manager is nigh on impossible to work with. I'm thinking things like...
Scroll down the list, select an entry, press the "move up" button, and be frustrated as the list bounces to the top with each button press. Guess a few times, scroll down to see how you did, count how many presses you went too far, press the move down button that many times, scroll down to check you have it in the right place now!
Support nesting or second level menus in the list to help us group them by media type or tree location or whatever we want.
Track the entries. If I add a view to favourites, then alter its name in the tree, favourites does not keep up with the alteration and that shortcut is now broken. As the manager does not allow us to edit the path, it must be deleted, then a new one added, and shuffled into place using the up/down guessing game mentioned earlier.
The manager window is not resizeable.
Think that's it... anyone else?