I have been using the site audit tool for a little while now and I have to say that it has some very nice features, including a very easy view of how your site architecture is being used (internal links).
It is still in beta, but I think a lot of people are going to like this. Easy to use, fast and without frill, that makes it easy to see what issues there are.
Definitely going to be another audit tool I add to my arsenal :)