For displaced Chicagoans in the Bay Area...
Agree with original Uno and Due at the top of the list...though watch out for that sausage. I never, ever get heartburn except after eating sausage pizza there. So if you're prone, you might want to stick with veggies. Spinach is better than it sounds, too.
In college (Evanston) I got by on Giordano's often. A very, very solid option but not the best around. Ditto for Edwardo's and Connie's. Will have to try Silo next time I'm there, sounds promising.
For those Chicago expats in the Bay Area, try Zachary's in the East Bay. (Locations in Berkeley and on College Ave. in Oakland.) Best tomato sauce ever, with fresh tomatoes on top. The best Chicago pizza not located near an El stop. Crust can't match Original Uno cornmeal crust, but what can??