Milwaukee CC, originally in the city but moved to the village of River Hills, is awfully good (Alison; see Ran's GCA review).
Ozaukee CC, in the county of Ozaukee in the northern Milwaukee suburbs, is a Langford-Moreau that's pretty darn good with a very good set of greens and some great use of the land.
Maple Bluff CC, in the bedroom community of its name next to Madison, is certainly the best (and only!) course in the village of some 1,400 residents. Tweedie originally with lots of redo's over the years. (Interestingly, although a private club, MBCC sits on land owned by the village, and thus village residents can utilize club facilities at certain times, including three rounds of golf annually.)
Sparta, a real mecca for bicycling in these parts, and a town about 30 miles east of LaCrosse, operates one of the better muni's in western Wisconsin.
My nine-hole home course, oddly enough, is part of the Madison muni golf system, and in the city limits, but is named for the suburb where I live and to which it is adjacent: Monona GC.
Erin Hills, host of the U.S. Open in 2017, is technically in the town of Erin and is quite hilly -- does that count?