I've found that the prototype is an excellent way to communicate with the client what it is you're going to build for them, and to get their input on how they think it could be better. People will not read functional specifications, but they'll interact with a prototype.
Our team builds the prototype in such a way that we can start building the app directly from the prototype, which we've tweaked after several interactive dog-and-pony shows with the client.
If your doing any kind of web application prototyping you should look at Snapp MX (www.snappmx.com). Snapp MX gives you the ability to create complete web applications through your web browser.
Here is an interesting excercise in usability : Task Management
Regarding prototyping, I put together a tool that may prove useful for some of the folks interested in the topic of this post. The tool is called spinetail and is released under a BSD license at google code. Spinetail is a rapid web application prototyping tool written in JavaScript. It is not a complete framework, but rather a tool to help web developers bring a static concept into a useful, living breathing format before deciding on technologies, and without configuring a development environment. Runs entirely client side, and is easily distributable.
More info here: Spinetail
Miha: I'll be delving into technologies and programming languages probably next week or the week after. Next up in the series will be database design. As well, I'll probably go into some further explanation of the design choices made in the HTML prototype.
At this very moment, I haven't made a decision which language and platform to develop in.