I've had a lot of pizza in Madison. There are a LOT of choices. But I will say Buck's is probably the best thin crust pizza around. They've been doing thin crust pizza for over 50 years - they've got it down.
It's a bit pricey for what you get (a deluxe/supreme runs about $20) but it is worth it. My favorite is a deluxe (no anchovies) - your standard cheese, pepperoni, sausage, mushroom, onion, black olives & green olives with a rich, hearty Italian sauce. This pizza is great fresh or frozen (they only do carry-out) but it's also killer re-heated for lunch or dinner!
If you're looking for very bread-y pizza, then Buck's will not please you - try Pizza Brutta or Glass Nickel for that - but otherwise, these guys & gals do thin crust just the way you want it!
Only complaint: wish there was another one downtown. The locations definitely don't get them any student business (right on Univ Ave near Middleton or out on Cottage Grove Rd), but they seem to do just fine!