There's like 3. Pepe's, Sally's, and Modern. They're so good that people from around the country come to my state (which is the most boring state in the world) to eat at those places, because they're supposedly some of the best in the country.
Just about any local pizza shop in the tri state area would just win over any place in Austin. Best place I have found here though is a tiny place called Little deli and pizzeria. They have got good sandwiches too. They are no sarcones, but still pretty good.
hmm.. best pizza would be Slices. It's a late night pizzaria right next to ASU. I go there all the time when I'm out by the university partying cause they are open til like 0400 or something like that, long after the bars close. great food, reasonably priced, and you can sit and sober up after a long night of drinking so you don't have to try to drive drunk.
If you want a good pizza you have to go to Naples, where you can find the best pizzas... I'm italian, and last summer I ate pizza there, it was the best ever.