I recently came across Balsamiq, a very well done application for quickly mocking up UI prototypes. With simple drag and drops you can quickly create some pretty slick prototypes. The prototypes have a sketch like look which allows the viewer to use more of their imagination, something I think is a subtle, yet powerful advantage.
It’s been a while since I’ve been so impressed with an app right out of the box… especially a Flash app. Just about everything works as I’d expect, right down to common keyboard shortcuts. It’s got good organization in it’s "ribbon" and so far it’s had just about every type of thing I need. It looks like it has JIRA and Confluence support, though that’s a bit on the pricey side. The Desktop version is reasonably priced though, and the web version seems to be free to use if you can put up with a nag every 5 minutes.
Nothing beats a whiteboard if you’re all in the same office, but I’d say this is a close second. Certainly better than Visio