Nice little writeup about desktop and online wireframing tools. At Clearspring, Jeff Wong and I use OmniGraffle pretty much end to end. I'll do concept diagrams and page flows with OG, and all of our page templates use the 960 grid to lock up wireframes and page mocks. We'll occasionally use Photoshop for more complex images, but the great thing about OmniGraffle is that we can use one application collaboratively from IA to UI to visual design, and move fast fast fast.
In previous jobs at Netscape and AOL, we'd use the Adobe Suite – Illustrator for diagrams and wireframes, Photoshop for visual design. What tools does your team use?