Spankomatic, my partner would have been one of the people complaining about headaches. We've had to stop going to many restaurants and other places due to CFLs. At first I thought it was too bizarre to be true, but now I know it's not: CFLs trigger his headaches. A good friend of ours who works in a Lyon's restaurant said they went back to incandescents for this exact reason.
The moment we walk into a room that's using them, he starts complaining about flickering. I never notice any. He does. Even if these CFLs are inside enclosures and you can't see what bulb type is inside, he's never once been wrong about it.
I hope that, for the sake of people like him, both bulb types continue to be readily available. We've already stockpiled a few dozen incandescents just in case.