I heard about a tool which seems to be helpful to design prototypes that help design web applications when functionalities are still not final.
I believe it is a good alternative to a static prototype that has been coded by hand in HTML. But I guess other tools like Dreamweaver can help making prototypes with better designs.
For quick and interactive designs with the customer, i also heard good things about the Powerpoint prototyping toolkit. Also, these series on building a complete web app from scratch seem like a must-read.
It is not a free tool but it is not too expensive. I played with it a bit, here are a few screenshots :