Apple has updated a patent that they already held featuring a sort of a Magic Wand -- a remote control for operating a media system by controlling an on-screen cursor. That might sound familiar if you own a Wii -- even the pictures look very similar to the way the Wiimote currently works. And the pictures tell us something else: not only does the patent itself mention a "media system," but the user interface looks very similar to the current Front Row interface on the Apple TV. So it's likely that if Apple is updating this patent, they're working on a new remote to control their set-top box.
But that doesn't mean it's the only thing they'd use a motion controller for -- I speculated a long time ago that Apple might want to put their now substantial App Store library into play on another platform, and a motion controller would go a long way towards replicating the touchscreen and accelerometer capability of the iPhone. Of course, this patent only means Apple is playing around with these ideas, not actually releasing hardware based on them. But it just shows that they're thinking along the same lines in terms of improving the browsing and interface experience.