Haven't been in several years, but used to go there often on business. Locals took me to several places, but my favorites were Kalmes in St. Donatus and Three Mile House across the river from downtown in Hazel Green, WI. St. Donatus is 15 minutes or so south of Dubuque. If you want a taste of local color, these are the places to go.
No website for TMH, but found these reviews in yahoo travel:
BTW, it's called Three Mile House because it's three miles from the MS river.
The only pizza I had was from Happy Joe's, which is now a sizeable mid-western chain.
Hope this helps!
Edit: Don't know what happened to my links, but just google both and you'll find the info.
post edited by Johnscreek - 2011/07/24 18:28:05