If the cause of the sore is allergic reaction, it might be sensible to treat it with antihistamines and steroids: benadryl capsules by mouth, hydrocortisone 1% ointment topically. Topical Benadryl (lotions and salves) seem to be more of a marketing gimmick than an actual treatment. Both benadryl and steroids are commonly used in the ER for allergic reactions. Some interesting thoughts on canker sores here (http://www.animated-teeth.com/canker_sores/t3_canker_sore_remedies.htm

Sores in the mouth are a symptom of scurvy; supplemental vitamin c might help prevent such. Avast, ye scurvy rogues-