According to HowStuffWorks, natural repellents than can be used to keep skunks away include oil of mustard and moth balls. These two products are especially effective in keeping skunks away from your garbage. Simply place the oil and moth balls at the bottom of the garbage can.
An effective repellent to keep skunks away from vegetable gardens is a solution of water and hot pepper. Skunks are also naturally repelled by cucumbers and squash because of their prickly leaves. If these types of plants are planted around other vegetable plants, skunks are less likely to forage for food in that area. A skunk can be ousted from its den by spraying the den with a mixture of boiled onion, jalapeño pepper, cayenne pepper and water. The smell of ammonia is also effective in repelling skunks.
Changes in daily habits can also help to keep skunks away. For example, garbage cans need to be kept firmly covered in order to prevent skunks from rummaging through the trash. Trash cans should be secure and difficult to knock over. Pets should be fed indoors to prevent skunks from being attracted to the pet food. Lawns and yards should be kept free of junk and wood, where skunks like to build their dens.