I've always been partial to Bacino's stuffed pizza (in Lincoln Park, on Lincoln Av) but I haven't had it in years.

There's also a new deep dish pizza place in our hood, Milly's Pizza in the Pan, that gets rave reviews and is quite good. I think it's a little salty, though. Be sure to order a day or two ahead - they sell out quickly. Oh, but if you show up without ordering they do make individual-size pizzas that are not sold online so you have a better chance of getting one.