Evil Mad Scientist has a detailed guide on making edible googly eyes for cupcakes, cookies, and other baked goods.
The trick lies in using edible gelatin capsules cut down into eye domes, with jumbo round sprinkles as pupils. Sprinkles go in the cut-down capsules, and capsules are affixed to an appropriate substrate: It "needs to be sturdy, so that it can support the rest of the eyes, light in color, and completely dry and free of oil. At the same time, it needs to be soft enough that we can press the gelatin capsules into it."
Whoppers cut in half seem to make an ideal substrate. For the complete how-to, step into the EMS laboratory.