3D Motion controller are the future in gaming and also for interacting with other computer software. Made popular by Nintendo in the Wii console it is now on the plate for other major computer and video game makers. Microsoft showed Project Natal at the E3 and Sony also showed their motion controller future.
Apple is apparentely also working on motion controller hardware and software as new patent filings appeared according to AppleInsider.
This is not the first filing from Apple about 3D motion controllers. Looks like it is a bigger effort at the company. The new filings are about 3D user interfaces for video navigation.

Additionally Apple filed some motion tracking patents for interacting with Mac OS X. See details on Apple Insider.