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Apple Insider posted a story that Apple's latest beta of iOS 6 for the Apple TV allows users to customize and reorder the layout of application icons, just like on the iPhone and iPad.

Similar to the long press used to move icons on the iPhone and iPad, users simply hold down the select button on Apple's remote while an icon is selected. Once this is done, the selected will begin to wiggle, and it can be dragged to a custom location on the TV screen.

In current, public builds of the Apple TV operating system, holding down the select button will put the device to sleep. Icons on the screen are also displayed in a static grid and cannot be moved.
  iOS 6 beta for Apple TV allows customizable app icon layouts