Well, hmm...no other symptoms. Are you ovulating? If you are, it could be 'mittelschmerz' which is pain with ovulation. If the pain disappears soon, start keeping track on a calendar when it occurs. Most likely it will be every other month.
Does it occur after having dairy products? You could be lactose intolerant.
If the pain doesn't go away, the pain could be the beginning symptom of kidney stones, a hernia, gastroenteritis, colon polyps or diverticulitis or like you said, a pulled muscle or an ovarian cyst. Have you fallen lately? Since the pain only comes when you yawn or take a deep breath, perhaps it's a hairline fracture to your lower rib?
If the pain becomes severe, go to your physician and have it checked out right away even if you're not having any other symptoms.