I'd go back to Clarke's which among made-to-order burger joints is a full notch above, say, Kirk's (the one that serves canned mushrooms and a condiment bar that closes down at 1:30--though they'll still shamelessly still sell you burgers at that time leaving you stranded without mayo, lettuce and everything else you'd expect with a burger). However, considering the family experience, convenience and overall value, I still prefer In-N-Out.
Clarke's also offers a complete breakfast menu featuring staples such as omelets and pancakes.
Clarke's Charcoal Broiler
615 W El Camino Real
Mountain View, CA 94040