Now to Wisconsin. And seriously, the highways in this state take some strange paths. I never would've thought of tying together Withee and Edgerton together with the same route number.
I don't see any routes that cross the state that don't miss at least one county seat along the way. I'm just naming off the seats themselves as it's easier.
US-2:
Hits: Superior, Ashland
Misses: Washburn, Hurley (barely - you could argue for a hit here)
US-8:
Hits: Barron, Ladysmith, Rhinelander, Crandon,
Misses: Balsam Lake, Phillips, Merrill, Marinette
US-10:
Hits: Ellsworth, Durand, Neillsville, Stevens Point, Waupaca, Manitowoc
Misses: Alma, Whitehall, Black River Falls, Wisconsin Rapids, Oshkosh, Chilton,
Hwy 11:
Hits: Monroe, Janesville, Elkhorn, Racine
Misses: Lancaster, Darlington
US-12:
Hits: Hudson, Menomonie, Eau Claire, Black River Falls, Mauston, Baraboo, Madison, Elkhorn
Misses: Neillsville, Sparta, Jefferson, Janesville (just barely touches Rock County),
Hwy 13:
Hits: Washburn, Ashland, Phillips, Medford, Wisconsin Rapids, Friendship,
Misses: Superior (barely), Wausau, Neillsville, Stevens Point, Baraboo
US-14:
Hits: LaCrosse, Viroqua, Richland Center, Madison, Janesville
Misses: Baraboo, Dodgeville, Elkhorn
(WisDOT doesn't acknowledge it ever enters Crawford County)
Hwy 16:
Hits: La Crosse, Sparta, Mauston, Portage, Waukesha, Milwaukee
Misses: Baraboo, Juneau
US-18:
Hits: Prairie du Chein, Dodgeville, Madison, Jefferson, Waukesha, Milwaukee
Misses: Lancaster
Hwy 21:
Hits: Sparta, Wautoma, Oshkosh
Misses: Mauston, Friendship (just barely)
Hwy 22:
Hits: Oconto, Shawano, Waupaca, Wautoma, Montello
Misses: Portage
Hwy 23:
Hits: Darlington, Dodgeville, Montello, Fond du Lac, Sheboygan
Misses: Baraboo, Friendship
Hwy 26:
Hits: Juneau, Jefferson, Janesville
Misses: Oshkosh (though historically it hits), Fond du Lac
Hwy 27:
Hits: Hayward, Ladysmith, Black River Falls, Sparta, Viroqua, Prairie Du Chein
Misses: Superior, Washburn, Chippewa Falls, Eau Claire
Hwy 29:
Hits: Menomonie, Chippewa Falls, Wausau, Shawano, Green Bay, Kewaunee
Misses: Ellsworth, Hudson, Neillsville
Hwy 32:
Hits: Eagle River, Crandon, Green Bay, Chilton, Port Washington, Milwaukee, Racine, Kenosha
Misses: Rhinelander, Oconto, Shawano (for the pedantic), Manitowoc, Sheboygan
Hwy 33:
Hits: La Crosse, Baraboo, Portage, West Bend, Port Washington
Misses: Sparta, Viroqua, Mauston, Juneau (near miss)
Hwy 35:
Hits: Superior, Siren, Hudson, Alma, La Crosse, Prairie du Chein, Lancaster
Misses: Balsam Lake, Ellsworth, Whitehall, Viroqua
I-39:
Hits: Stevens Point, Portage, Madison, Janesville
Misses: Wausau, Wautoma, Montello
US-41 (standalone):
Hits: Marinette, Oconto
US-41/I-41: Green Bay, Appleton, Oshkosh, Fond du Lac, Milwaukee, Kenosha
Misses: Juneau, West Bend, Racine
I-43:
Hits: Green Bay, Manitowoc, Sheboygan, Port Washington, Milwaukee, Elkhorn
Misses: Waukesha, Janesville
US-45:
Hits: Eagle River, Antigo, Oshkosh, Fond du Lac, West Bend, Milwaukee
Misses: Rhinelander, Shawano, Waupaca, Appleton, Waukesha, Racine, Kenosha
US-51:
Hits: Hurley, Merrill, Wausau, Stevens Point, Portage, Madison, Janesville
Misses: Eagle River, Rhinelander, Wautoma, Montello
US-53:
Hits: Superior, Chippewa Falls, Eau Claire, Whitehall, LaCrosse
Misses: Shell Lake, Barron (just barely)
Hwy 57:
Hits: Sturgeon Bay, Green Bay, Chilton, Port Washington, Milwaukee,
Misses: Kewaunee, Manitowoc, Sheboygan
Hwy 60:
Hits: None!
Misses: Prairie du Chein, Richland Center, Baraboo, Portage, Juneau, West Bend, Port Washington
US-61:
Hits: LaCrosse, Viroqua, Lancaster
Misses: Prairie du Chein
US-63:
Hits: Ellsworth, Shell Lake, Hayward,
Misses: Hudson, Balsam Lake, Barron, Washburn, Ashland
Hwy 64:
Hits: Medford, Merrill, Antigo, Marinette
Misses: Hudson, Menomonie, Chippewa Falls, Oconto
Hwy 67:
Hits: Elkhorn,
Misses: Janesville, Waukesha, Juneau, Fond du Lac, Sheboygan, Manitowoc
Hwy 70:
Hits: Siren, Eagle River, Florence
Misses: Shell Lake, Hayward, Phillips, Rhinelander, Crandon
Hwy 73:
Hits: Neillsville, Wisconsin Rapids, Wautoma
Misses: Ladysmith, Medford, Stevens Point (for the pedantic), Montello, Green Lake, Portage, Juneau, Madison
Hwy 80:
Hits: Richland Center
Misses: Wisconsin Rapids, Mauston, Viroqua, Lancaster, Dodgeville, Darlington
I-90:
Hits: LaCrosse, Sparta, Mauston, Madison, Janesville
Misses: Baraboo, Portage
I-94:
Hits: Hudson, Menomonie, Eau Claire, Black River Falls, Madison (barely), Waukesha, Milwaukee, Kenosha
Misses: Whitehall, Sparta, Baraboo, Portage, Jefferson, Racine
US-141:
Hits: Green Bay
Misses: Marinette
(Historic) US-141:
Hits: Green Bay, Manitowoc, Sheboygan, Port Washington, Milwaukee
Misses: Marinette
US-151:
Hits: Dodgeville, Madison, Fond du Lac, Chilton, Manitowoc
Misses: Lancaster, Darlington, Portage, Juneau