Amici's is pretty good if you're into New York style. Several locations all up the peninsula, but not enough to turn it into a Dominos/Round Table/etc type joint.
Windy City pizza in San Mateo is pretty good too.
Someone else mentioned Extreme already, another pretty good place.
I remember "Escape from New York" in the Mission to be a good spot as well, but that might have just been a side effect of the entire night being awesome.
Finally, at 3 AM, Mr. Pizza Man. It's not the greatest, but at that hour you're probably too drunk to notice.
For deep dish: Zachary's Chicago Style Pizza Their spinach and mushroom is great and don't be afraid of it if you don't like mushrooms. A lot of people like it who hate mushrooms
Thin crust: Arizmendi They only have one pizza a day and it is vegetarian, but make it work.
For parties: Costco Giant pizza 9.99 and it still taste pretty good.
Everything Else: Pyzano's Pizzeria All their Pizza's are great. I really enjoy the pesto and Tomatoes.
Don't judge by all the veg pizza I prefer my pizzas covered in ham, bacon, and sausage, but when a pizza is good who cares if it is a veg pizza.
Well, I grew up here, but lived in New York for almost 10 years. And after coming back, I must say, I still (in 5+ years) haven't found really good pizza. Zachary's is fine, Little Star is decent. But honestly, any ganky pizza place on the corner in NYC would blow 90% of SF pizza out of the water.
Not trying to be argumentative, just calling it like it is. I'd say the same thing about burritos in New York.
That said, Arnell's (on Valencia in SF or by the BART station in Berkeley) is the closest thing I've found to real NYC pizza. So that's where my vote goes.
For NY Style thin crust its gotta be Lanesplitters in Berkeley (a very cool place!).
For Chicago style deep dish, without a doubt, Zachary's in Berkeley/Albany.
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