The late Borderline Pizza in Chester, Iowa is the best I've ever had. Their recipe lived on at R&B Pizza in Osage which has been recently bought by a new owner and renamed. I don't know what the new name is, but I'll be looking to try it out sometime.
Mabe's in Decorah is probably my favorite currently. They deliver to Toppling Goliath's tap room. Hard to beat that pizza/beer combo.
In central Iowa, Pizza Pit and Jeff's are among my favorites in terms of overall pizza quality. Fong's and Big Tomato have the best topping combinations, but probably aren't as good in terms of sauce/crust.
Eastern Iowa, gotta go with Falbo's in IC. Every time I partied there, the night couldn't end without a giant $2 slice of Falbo's.