In Pacific Beach there is a wonderful breakfast place called The Broken Yolk. We loved it, it doesn't look like much best is some of the best food we found. This is from a restaurant review I found on it:
With more than 20 omelets on the menu, this cafe does break a lot of yolks. On weekends, you'll find folks re-fortifying constitutions that were wasted during the week's labors or wetted in the previous night's reveling; and on weekdays, locals who seem in no hurry to be off to work. There's a dare-you type special on the menu: It uses a full dozen eggs and costs under $2 if you finish it in a hour. The lunchtime menu includes burgers, patty melts and anything else that you can cook on a grill.