I use a combination of Balsamiq and Illustrator or Photoshop. I whip out the basic design in Balsamiq. It's so lightweight and fast that can iterate quickly on the wireframe. Once I know what the layout is, I re-draw it in Illustrator (if I'm writing the markup myself), or Photoshop (if I need to pass off to a graphic designer), to work out the colors, fonts, and styling.
What I love about Balsamiq is that it limits your choices- you only have 1 font, few colors, and a list of elements. It forces me to concentrate on the layout, not whether things should be in helvetica or lucida, pink or blue.
I've used OmniGraffle for flow diagrams and find it cumbersome (though it gets the job done). Installing Yahoo stencils sounds like work I'd like to avoid.
Powerpoint is probably the most painful program that exists. Yes, many people know how to use it, but you have to do so much manipulation to get what you want on the screen. And it takes 5 min to open. I'm an MBA and have found it so frustrating that I learned Keynote and InDesign so I'd never, ever, have to open that beast of a program again.