In SF, I prefer Flour + Water. Reservations are a joke, but if you get there between 5:30 and 6 you can snag a table at the bar. Coming from the three time zones away on the first night we actually didn't mind eating earlier since we were starving. I've been three times, but never had the opportunity to sample the bone marrow pizza.
As many have documented here, Tony's in North Beach is something to see. Something like four different types of ovens.
Pizzeria Delfina (which is different than just regular old Delfina which the more formal restaurant next door is good as well. I have no pictures because it was 93 degrees the night we ate there and I just wanted to eat and get out. It was HOT! . I now know that most of SF is un-air conditioned. It's a tight little spot but tables turnover quickly.
Surprisingly I liked Gialina. When I saw the pizzas coming out, I was like, "Oh man, these things do not look very good." The dough was actually very good. This is a little off the beaten path, but was worth the trip.
[Flour and Water first pics] [Gialina last three]