I'm a big fan of Extreme Pizza--by the slice, in the store. The delivery is almost as good. Some people say Pizza Orgasmica is the best but those must be extremely rich folks who don't mind spending over $20 for a small pizza. Holy crap! And it wasn't even that good.
Little Star pizza has a few locations in SF, and is also very good.
X2, They are awesome. It kills me that my girlfriend only really likes thin crust 'cause the deep dish there is great. I've only been to the one in the mission, on Valencia I think. Can get crowded there, if you don't catch them at a slow time, expect a short wait, but up to ~an hour around 8ish on a friday.
For some peculiar reason it was on my mind so I had little star for dinner. A little pricey but some damn good pizza compared to the chains. Bad cell phone pic but gives you an idea of how deep the deep dish is. And not doughy at all, it's still crunchy underneath all that topping.
Well, if im in the mood for deep dish, I have to agree with Amy, Old Chicago is fabulous. However if I want a thin crust, you cant beat Giovannis in Cotati. Talk about a good pizza, both these places are must tries.