definitely Jake's in Del Mar, Roy's in LaJolla ($$$$), Valentina's Restaurant - best ceviche con camarone i've ever had as well as Pollo asado tacos
in Escondido, Peterson's donut shop in Escondido as well...
Most importantly you've got to make the drive out to beautiful, quiet and quaint Julian, Ca for their APPLE PIE just northeast of san diego.
George's at the Cove also...