This may be too simple a solution for you, but I was listing to the Boagworld Podcast, and they reviewed a wireframe software package called
Oversite - Wireframe and Architecture Software for Software and Web Designers and Developers
I tried it myself, and I decided I liked using Visio for what I was doing at the moment. Visio doesn't have the site architecture functionality. If I remember this does. It is also free. Again, I didn't get into it very far to tell you how functional it is, but it is worth taking a look at.
Good luck.