I ran across a tool called Lucid Spec that allows you to do rapid screen prototyping with clickthrough capabilities. They bill it as a tool for creating better specifications, which it would invariably be in the hands of a good user experience designer.
It could also be a tool for making higher fidelity "paper prototypes", although that can backfire on you. When doing paper prototyping, it actually helps you get better user feedback if you have rough sketches that don't look too polished.
However, after the paper prototyping phase, this Lucid Spec tool could be quite useful for showing the developers what to develop and how it should work.
Resources on paper prototyping: