The La Crosse City Brewery, which used to be the G. Heileman Brewery, has a fun tour. I lived in La Crosse for two years, and had friends who worked hospitality. Being a minor, I was grateful for their lax enforcement of ID laws, and they always brought the overages home. Their house was always stocked with tallboys, and I rarely paid for a drink my sophomore year. Pearl St. Brewing, also in La Crosse, makes a fine brew, but I'm not sure they offer tours.
Now, my office is a mile north of Karben 4 (just off I-90), and I haven't been. Additionally, I haven't been to the new Ale Asylum location, which is a half-mile away from Karben 4. If I didn't carpool, I'd have frequented both by now. I have a sneaking suspicion that there is a micro in Verona, which is a few miles out of Madison, but I have no proof.
I believe Mount Horeb has a brewery, and Monroe definitely has one, possibly two.
I wish there were a brewery-town high-speed rail network in Wisconsin.