Prezi is the shit (in a good way).
That's what I use to lay out my wireframes. Because it allows me to zoom in and out almost infinitely, I can zoom in to lay out all my pages with all the details and zoom out to see the overall structure and flow.
Its drawing tools are a little clunky, so I just use indesign to create all the elements and import them into Prezi.
I pay $13.25 a month so I can have a desktop version as well, but it's totally worth it.