We help our customers design and build apps - traditional and mobile. One of my personal favorite tools for prototyping is a notebook and pen, followed closely by a good big whiteboard. Its not "sexy" or "modern", but there's something about the act of actually drawing designs out with your hands that can really bring a new element to the design process.

As for the tool selection, without knowing what sort of app you're considering any recommendation would be premature. Feel free to give me a call, or post some follow-up information (could be vague - is it an action game or a contact management solution for example).