Frankie Johnny and Luigi Too is my favorite pizza ever, anywhere. 939 West El Camino Real, Mt View http://fjlmountainview.com/
Thick but crispy crust, light and fresh tasting sauce, rich cheese and loads of meat and veggies. Try the Stromboli or Tina's Too Too Much. The interior is beautiful and romantic, and it's easy to imagine you're in a little Italian place off a dusty road in the countryside. They just got a full bar, which doesn't hurt.
Running a very close second is La Trattoria Bohemia, 3649 J St, Sacramento http://www.latrattoriabohemia.com/
Same type of pizza in a combo Italian/Czech place. Their spinach ricotta gnocchi with gorgonzola, proscuitto and mushrooms must be tried as well. And it's right next door to Bonn Lair, the best and friendliest pub in the city.