Denim (http://dub.washington.edu/denim/) is kind of interesting. It's a Java Application with an "interesting" UI (seems a bit ironic). It's probably worth a few minutes of downloading and checking out to see if it suits your style.
Personally (and I'm more of developer than a designer), I'm with wammin, pencil paper or many white board sessions are where I start for the first few dozen iterations. The last thing I want is yet another tool to get in my way, providing more complexity than value. Once things settle down, or if you have to work with off-site people, electronic versions make a lot of sense.
Denim rocks. Paper & pencil rule, but Denim makes it easy to get a working mock-up up and running.
After drawing out the pages, you can create active links among them, and export the site to HTML. Denim creates pages that have nothing more than image maps, with hot spots for linking and navigating around the site.
This is something you can run in browser and put in front of clients to verify general behavior and layout.
Plus I like how you can zoom in and out to see a site map or a single page or some detail in a form on page.
Note: Denim works best with a drawing tablet, such as what Wacom sells. But a mouse will work as well; the gestures, though, may be harder to execute.
Personally (and I'm more of developer than a designer), I'm with wammin, pencil paper or many white board sessions are where I start for the first few dozen iterations. The last thing I want is yet another tool to get in my way, providing more complexity than value. Once things settle down, or if you have to work with off-site people, electronic versions make a lot of sense.