The patent is nestled in amongst several others relating to NFC controls for the iPhone and other devices, including a TV.
It would work wirelessly using RFID and NFC tags, effectively turning Apple TV into a games console (with games, obviously, already available in the Apple App Store).
Like most Apple patents though, it's possible that this is a red herring or simply a line of research that will come to nothing.
But with speculation of an Apple HD TV reaching fever pitch, it's just possible that a gaming controller could be a realistic peripheral.
One thing the patent filing does seem to point to is that Apple is at least seriously considering including an NFC chip in the iPhone 5.
From Patently Apple