You should check your cat's eyes and ears periodically for any type of coating or junk.  Ears should always be clean with no type of build-up.  To clean your cat's ears, use a Q-tip or warm wet cloth and clean around inside the ear only near the outside, but never enter the ear canal.  If you notice any difference in the ear canal, notify your vet.  Brown build-up could be ear mites, a parasite that needs to be treated as soon as possible.

Occasionally your cat may get brown crusty-looking material in the corner of his eyes - this is fine, it's similar to the white "goop" humans get in their eyes in the morning.  Clean with a Q-tip dipped in warm water.  If the area looks different than it usually does, or if the discharge is white, clear, yellow, or green, schedule an appointment with your veterinarian.