The basic tool for rapid prototyping is, as you might know, a white board and good User eXperience Design (UXD) principles (in your head).
Your favorite IDE could serve the purpose (you already know how to implement Grahical User Interfaces there, so there's no ramp up). Sparx Systems' Enterprise Architect also allows you some basic prototyping (and navigation) with the advantage of traceability of UI elements to other elements of the model (such as requirements and tests).
Any image editor also could do (as well as some sheets of hand-drawn papers that after peer review could be quickly scanned and added to the Version Control System or to meeting minutes). The only problem with these latter tools is the need of navigation (between windows, pages) so that the visualization of the final system behavior is easier.
There are however specialized tools for rapid prototyping like Balsamiq. Some are free, some other are not. Some are specialized for Web applications, some for mobile apps, some for client apps.
A good review of some of these tools can be found here:
