Visio is an excellent prototyping tool. Probably the one I turn to most. This is in no small part due to some great free templates that make generating mock ups so quick and easy. Here is a list of some of what's on offer - all free to download.
I've used the GUUUI stencils for years with great success. If you've never done this kind of thing before, it's a great place to start as the stencils come as part of a really good tutorial.
Visio: the interaction designer's nail gun (3rd edition) - GUUUI stencils and tutorial
A few other templates and resources for prototyping with Microsoft Visio:
Swipr plugin for Visio - enabling HTML outputs
Visio wireframe toolkit - by Bill Scott in his Looks Good Works Well blog
Visio stencils by Nick Finck