Something got me thinking about this for Wisconsin. No brainer, right? Barry Alvarez. Or is it?
"King Barry" resuscitated Wisconsin football, won three conference championships and three Rose Bowls (still the only ones Wisconsin has won), and had several top-10 AP finishes. As the head football coach he went 8-3 in bowl games (and is 9-4 overall, having coached two more on an interim basis as the AD). In sixteen seasons ('90-05), he had a .605 winning percentage, which isn't gaudy, but taking into account where the program came from, it's pretty darned impressive. And he brought in Ron Dayne, Wisconsin's second Heisman Trophy winner. Also while still the coach he brought in Bret Bielema and brought Paul Chryst back (this is as a coach; as the AD, his hires look pretty good, too).
In seven seasons ('06-'12), the much-reviled Bret Bielema had a winning percentage of .739, won three conference championships, and his teams made three appearances in the Rose Bowl (but lost them all, though Alvarez coached the last--and least deserving). His teams were 2-4 in bowl games (2-5 with the Rose Bowl Alvarez coached when Bielema left), but, again, seven bowl games, including three Rose Bowls, in seven seasons [H/T to Badge for pointing out where my math wasn't adding up.]. And he left the program in pretty good shape, as evidenced by Gary Andersen's .731 winning percentage in his two seasons.
BUT...
Ivy Williamson went .641 in six seasons ('49-55) in Madison, including a Big Ten championship and appearance in the Rose Bowl (a 7-0 loss to USC)--in an era in which only the conference champion played in a bowl game. He also brought Alan Ameche--the only other Badger to with the Heisman, to Madison. Also, like Alvarez, he became the AD after coaching, and brought in Milt Bruhn...
Milt Bruhn had a modest .505 winning percentage during his eleven years ('56-'66) in Madison, but he twice won the conference championship. Despite going 0-2 in the Rose Bowl, in the 1962 season he coached what is generally considered Wisconsin's best-ever team, losing a dramatic Rose Bowl to national champion USC, and finishing with the highest AP ranking of any Wisconsin team (#2 -- to be fair, at the time the AP didn't re-rank teams after the bowl games). Bruhn, too, became the AD (when Williamson retired), but passed--or missed--on the opportunity to hire some guy named Schembechler (you may have heard of him).
What about Dave McClain? He had a .506 record in eight seasons ('78-'85) in Wisconsin, but like Alvarez was brought in to fix an anemic program. He turned around Wisconsin's fortunes, including four-straight winning seasons, and five of eight after Wisconsin had only one winning season in the fourteen seasons before he arrived. He went 1-2 in bowl games giving the Badgers their first ever bowl win (in the Independence Bowl over Kansas State). He died suddenly in April 1986, leaving the Badgers without a head coach.
There are some guys back in the Michigan era of college football, but I can't even begin to think about them.
And Paul Chryst currently has a remarkable .829 winning percentage and is 3-0 in bowl games, including two "New Years Six" bowls, after three seasons ('15-...), but no conference championships and he has benefited from a weak B1G West. He "righted" the program that many thought Andersen left worse than he found it. But let's face it, it's early.
So I'll exclude Chryst.
After all that, King Barry keeps #1, due to his longevity and bowl record, but there's a good argument for Williamson at #2. Bielema, despite the ill-will towards him, did a good job in Madison. I place him at #3, but there's a good argument based on his conference championships and winning percentage to put him at #2. Bruhn finished with three straight losing seasons, and though it shouldn't count against him as a coach, did a horrible job finding a replacement for himself. That probably elevates McClain to #4, Bruhn at #5, and Chryst pending...
Honorable mention to Harry Stuhldreher, one of the Four Horsemen of Notre Dame, and the only Wisconsin coach to deliver any kind of recognized National Championship (1942 Helms Athletic Foundation--Ohio State won the AP national championship, with its only loss at Wisconsin). But his winning percentage at Wisconsin was .425, he only had three winning seasons, and he never won a conference championship in his thirteen seasons ('36-'48).
The 1942 season is a curious one. Ohio State won the conference championship despite the loss to Wisconsin and both teams having one loss in conference. But Wisconsin only played five conference games to Ohio State's six, thus Ohio State had a better conference record (5-1 to 4-1) and thus won the conference title. Ohio State finished the season 9-1 and was the AP #1/MNC, but did not play in a bowl game. Wisconsin, with "Crazylegs" Elroy Hirsch leading the team, was 8-1-1, AP #3, with the win over MNC Ohio State, a win over #19 (final AP) Minnesota, a tie against #6 (final AP) Notre Dame and a loss at Iowa. AP #2 Georgia defeated #13 UCLA in the Rose Bowl and claims 1942 as one of its two MNCs from an era in which the MNC was, well, mythical. Georgia's wins included whuppings of then #3 Alabama and #2 Georgia Tech, with its loss to that pesky Auburn.
PS: I don't swear all the winning percentages are exactly correct. FTBobs, where did you move cfbtrivia!?!