Pannikin Coffee & Tea
-- Pannikin Coffee and Tea -- I went to the La Jolla location but it turns out they have two others in the San Diego area. This cafe has great service and generous portions, along with the feel of the neighborhood coffehouse. I can only speak to their breakfast offerings - made to order scrambled egg dishes as well as fresh fruit and pastries - but I am sure that lunch is just as great.
-- Chart House -- Yes, they have locations all along the California coast and throughout the country, but the Cardiff location is one of my all time favorites. Chart House generally has great fresh seafood, and a wonderful salad bar, but the view that each restaurant offers is what completes the dining experience. I have been to many of them, and the only other view that compares is the one in Dana Point.