I haven't had a canker sore for a long time, but I remember that toothpaste works well for small ones. Just apply a small dab with your finger and try not to move your mouth too much for a few minutes.
I've tried the sealing stuff that Jixby mentioned for the larger canker sores that I've had, but I drool too much and it usually doesn't stick.
But it stings like hell and kills all the bacteria at least. eek