It may sound like a strange combination, but several dentists swear by this homemade remedy: Mix together equal amounts of Milk of Magnesia or Kaopectate and Benylin or Benadryl. Milk of Magnesia and Kaopectate both contain ingredients that coat wet tissues, such as those in the mouth. Benylin and Benadryl contain ingredients that act as mild topical anesthetics and antihistamines (which reduce inflammation).
Apply the mixture to the canker sore using a cotton swab. Be careful not to swallow the stuff; you could end up anesthetizing (numbing) the reflex that keeps the windpipe closed when you swallow.