Visio/Omnigraffle - you can export to a pdf or a selection of images & hack out a click through from there.
Balsamiq with this: http://eclecticguy.com/2008/11/06/assembling-demos-from-balsamiq-mockups/ while waiting for this: http://getsatisfaction.com/balsamiq/topics/help_me_design_the_linking_mockups_feature
Axure RP: http://www.axure.com/
I've used previous versions of Axure and while it was initially thrilling (hitting that sweet spot in between handcoding a click through & having the project features of a Visio-type program) I found the undesirable tendency for the tool to influence the designs. I'll be testing the latest version & if anyone is interesting i can let you know how that compares to the mix.
Adobe InDesign / Powerpoint - granted, this is the strangest method i know - but it can be rather effective used to build an (internally) linked document. Too bad every other part of that experience is clunky.
Beyond those above, there's always the code it from scratch and/or use a WYSIWYG approach. There's also paper and/or index cards - but for now I'm limiting the field to digital options.
My ideal tool of course gives me complete control to present the ideas quickly while not requiring me to get so far into their domain specific language that I lose perspective on the actual problem at hand. This seems to be the biggest danger with the 'from scratch' approach as you can of course to all sorts of wonderful things in an html clickthrough that have nothing to do with the work at hand. At the other end of the spectrum, though, a pdf presentation is quite quick - but not very interactive & subsequently not great for user testing.
Any secret (or not so secret) weapons out there? Seems like this could be an interesting emerging market...