JoAnn's is still good IMO, and still very crowded, get ther early to avoid long lines. Also very crowded and top notch (a chounds fav) is Nini's on the Burlingame/SM border. They have, by far, the best Greek omelette with tender succulent lamb.
There is a new place called SM Grill or Rotisserie (?) on B Street in SM (at 2nd) that has decent food and lovely service, although they are still getting their sea legs. My favorite breakfast in the area is at LaMichocan also on B in SM, with fabulous pupusas, tempting platanos con crema y frijoles, and of course, omelettes with chorizo and huevos rancheros.