  "The reason why Visio is the favorite prototyping tool of many interaction designers is because of its ready-made interface objects, you can drag-and-drop onto pages and its ability to link pages together and export them as web pages. But what distinguishes Visio from other prototyping tools is its use of layered backgrounds. " Visio is my tool of choice for site maps and urlLink wireframes , or anything I want to explain visually.
I have used Illustrator, but it really isn't built for site mapping and prototyping unless that is the only tool you know. The drag and drop capabilities and custom stencils of Visio is what I like best. However, the one thing that bugs me most is I need more layers, instead of being limited to one layered background. Of course I would need to move to an Adobe product to get that functionality. 
