I have used clicker training with great success in the past, particularly with a dog of mine that had dominance aggression. It truly changed his life.
However, I now have a dog that I believe was badly treated while training. I don't know his history because he is a rescue, but when I tried teaching him that the clicking sound was a good sound, I basically trained him to hate hot dog bits. He now shrinks away if I offer him a hot dog piece, even without the clicker. The sound of the clicker made him run and hide from me and refuse to come out for at least an hour. I don't know what he associates with this noise, but clearly it is not good.