I use a variety of programs for diagramming plays. For my own playbooks, I use Playmaker Pro from BW Software. I also use the CoachMe Football app for iPhone and iPad. (it's available for Droid and other platforms as well)
In the web clinics, I use a Wacom Bamboo Tablet to draw on a blank PowerPoint slide most of the time. It looks fancy because I use a blackboard background, I guess. But it's not.
I also use the BaiBoard app for Macbook, mainly because PowerPoint for Mac doesn't have an eraser function like the Windows version does.