My favorite pizza in Madison is hands down Ian's Pizza (www.ianspizza.com). They have a crazy selection of flavors, some of my favorite being their Chili Cheese Frito Slice, Guacamole Burrito, Salad Pizza, and they even know how to do a great, simple pepperoni slice. The price points are right, they sell them by the slice or you can get a huge 20" pie for as little as $13.
They also have a huge salad bar that features tons of local ingredients when they can. The best part of the salad bar is it's build your own, so you can make whatever kind of salad you want and then they toss it infront of you. Cool stuff.
Definitely check them out, they were voted Wisconsin's Best Pizza in by Food Network Magazine and have a great presence on Facebook (www.facebook.com/IansOnState).