I've used Visio for years to do diagramming and high-level layout and interaction.
This Autumn I'm using Omnigraffle. I'm also using rapid-prototyping tool Axure. To use PC-only (so far) tool Axure, I installed a virtual machine running Windows 7. VM is pretty cool, I have to say.
I am still learning Axure, but it looks like it makes it easier to show interactive features and simulate site features. Things like "type ahead", dropdowns, tabs and lots more. I have had luck finding instructional videos on youtube.
On the down-side, the codes that Axure creates is a bit of a nightmare. So don't plan on it being re-usable. Think of it as a "one-off" that will need to be totally re-created.
Omnigraffle, so far to me, seems nearly identical to Viseo. Bring on the firestorm/prove me wrong. I'd love to hear your views about the finer points of the differences.
Can't believe it's November already!