My dog is constantly shaking her head and flopping her ears from side to side. There is no visible infection in them or anything else that I can see. What could it be?

My first guess would be an ear infection. My dog was doing the same thing and I was surprised to learn how deep the ear canal really is. His infection was so deep that it was not visible. How long has your dog been doing this? I would see a vet if it isn't getting better.

She has been doing it for a few months. She used to scratch them really bad. Now she just shakes her head.

How do they smell? Take her to the vet. He will use something I can't spell with a light and a long rubber tip to look deep into her ears. Chances are, he will find an infection, and prescribe some antibiotics that will clear up the problem within a week. Some ear problems can be treated at home, but not an infection.

You need to see the vet, the scratching and flipping his ears is a sign of discomfort, ears are nothing to play with, take it from some one who knows now, do not take the wait and see approach. You pets health depends on you.