The Green Flash - located in Pacific Beach (PB), has great Huevos Rancheros (a mexican breakfast dish with tortillas, eggs, beans, and cheese).  They also have a wide selection of other breakfast/lunch/dinner items too.  Their beachfront dining is perfect for people or wave watching!      http://www.greenflashrestaurant.com/

George's At the Cove- in LaJolla Village, on Prospect.  There are two sections to this restaurant- a formal inside seating, or a casual rooftop seating.  The rooftop view is amazing and the food is moderately priced (for La Jolla) and pretty tasty.  Their fish tacos, gyro sandwich or any of their special pasta of the day are good choices.  The wait staff can be snooty at times.  http://www.georgesatthecove.com

Peohe's--on Coronado Islad. It's right over the bridge on Coronado facing downtown San Diego.  Wonderful view, great service and food.

On Harbor Island, with fabulous views of Downtown San Diego, sits Island Prime and its casual dining/bar C Level. C Level is a winner with attentive service and fabulous offerings. The nut crusted brie is one of several great starters and a lobster truffled mac and cheese is one of many great main dishes.

http://www.cohnrestaurants.com/