I am with you on Pie Factory. I haven't had a bad pizza from there yet. My favorite is actually not on the menu anymore but they will make it for you. It is called the El Blanco. Other than that, locally I'd say my second favorite is Pizza Chef, particularly their Mexican Pizza. All of the major chains are pretty similar to me, but I guess I would pick Pizza Hut if forced to choose one.
I will also travel to Huntsville from time to time just for some Mellow Mushroom, the Holy Shiitake to be more specific.