I just stumbled upon a very nice web/mobile application called Realizer. It allows you to upload sketches (single screens) of User Interface designs for iPhone or iPad to a web interface. You can then link these single screens by adding interactive areas in your sketch, such as buttons. Having finished your mock-up, you can download an iphone/ipad app to show the prototype to others on your handheld device.
I think you could not only prototype mobile apps with this tools but possibly also other complex designs, such as Service designs. It's worth exploring further at http://realizerapp.com/