Doppio Zero on Hayes by Davis Symphony was quite good, although a bit fancier. Amici's East Coast Pizzeria on Lombard in Marina was also very tasty. Also, it's not as fun, but Mountain Mikes is also great, inexpensive pizza, like in your Papa Johns range but better overall.
Arizmendi bakery has rotating toppings but is a ceaselessly classy slice.
North Beach has some good spots. My go to after a night of drinking is Golden Boy.