I use a Dremel tool with the thin round disc cutting attachment to cut a groove into the head of the screw, at which point it's often possible to use a flathead screwdriver to get it out. Just be careful not to cut too deep, because you'll run the risk of cutting half the head of the screw off, and then things are even more difficult.
In the case of the bottom casing of iBooks, I often end up just ripping the case right off when one of the three long screws won't come out, and then I use a heavy wrench to turn the screws and get them out once the casing has been removed. Fortunately the screwholes break off pretty cleanly, so it's possible to put the bottom casing back on later and it's not apparent (unless you look really hard) that damage has been done.