My favorite is Holders Country Inn. I used to go to the one in Cupertino before it burnt down. They moved, this was on Deanza long time back, and the one on Wolfe does not have the same old diner feeling, it is for the next gen :) Now I go to the one on Saratoga. And while I do not go as often to other places, I have been to and liked Hobees, then there is one Joe's near Half Moon Bay. We go there as a family when we hike at Cowell Purisima trail nearby. And while I am rambling about places to eat, a recent non-diner discovery has been El Caminito on El Camino Real.
Not OP but I'd recommend the Peninsula Fountain Grill in Palo Alto. Peter's Cafe isn't bad either if you've got time to kill near the Millbrae CalTrain station.