They
are.
1. Wake Forest
2. Indiana
3. Northwestern
4. Kansas State
5. Iowa State
6. Kansas
7. Oregon State
8. Vanderbilt
9. Duke
Very interesting. Although, I don't know if purely looking at winning percentage is necessarily the best way to determine the worst programs. Using college hockey as an example, is Boston College the best college hockey program because it has the top winning percentage? Is Clarkson better historically than Cornell because of the same? Are Princeton and Massachusetts the worst "Big 4" programs in history? Although, it certainly adds a piece to the puzzle, I don't believe it is the end all be all.
For college football, in addition to winning percentage, I would look at other factors, such as conference titles, bowl games, top 10 seasons, etc. And I would select a "champion" for each conference to get my bottom 5.
Let's start with the programs that have won 2 or fewer conference titles in the last 50 years:
ACC: Virginia (2), Boston College (1), Wake Forest (1), Duke (1)
B1G: Rutgers (1), Purdue (1), Indiana (0), Minnesota (0)
Big 12: Oklahoma State (2), Kansas State (2), Texas Tech (1), Kansas (0), Iowa State (0)
Pac 12: California (2), Washington State (2), Oregon State (1)
SEC: Kentucky (0), Ole Miss (0), Mississippi State (0), Missouri (0), USC (0), Vanderbilt (0)
Now let's rank these teams by the number of Top 10 seasons (using AP/Coaches Polls) in the last 50 years, and eliminate the top team from contention:
ACC: Boston College (2), Virginia (0), Wake Forest (0), Duke (0) - Boston College eliminated
B1G: Purdue (1), Minnesota (1), Rutgers (0), Indiana (0) - Purdue eliminated*
Big 12: Kansas State (6), Oklahoma State (4), Kansas (2), Iowa State (1), Texas Tech (0) - Kansas State eliminated
Pac 12: Washington State (5), California (2), Oregon State (1) - Washington State eliminated
SEC: USC (3), Missouri (2), Kentucky, (1), Ole Miss (1), Mississippi State (0), Vanderbilt (0) - USC eliminated
Then let's rank the remaining teams by the number of bowl games played in the last 50 years, and keep only the bottom two teams in contention:
ACC: Virginia (21: 8-13), Wake Forest (14: 9-5), Duke (8: 3-5) - Virginia eliminated
B1G: Minnesota (20: 9-11), Indiana (12: 3-9), Rutgers (11: 6-5) - Minnesota eliminated
Big 12: Oklahoma State (28: 18-10), Texas Tech (27: 13-14), Iowa State (15: 5-10), Kansas (9: 5-4) - Oklahoma State and Texas Tech eliminated
Pac 12: California (16: 10-6), Oregon State (12: 7-5)
SEC: Mississippi State (22: 12-10), Missouri (22: 11-11), Ole Miss (19: 14-5), Kentucky (17: 9-8), Vanderbilt (8: 3-4-1) - Mississippi State, Missouri, and Ole Miss eliminated
Then let's compare the bottom two in each conference by winning percentage:
ACC:
Wake Forest (41.9%) vs Duke (48.8%)
B1G:
Indiana (42.1%)vs Rutgers (49.3%)
Big 12:
Iowa State (45.7%) vs. Kansas (46.9%)
Pac 12: California (55.0%) vs.
Oregon State (47.2%)
SEC: Kentucky (50.2%) vs
Vanderbilt (48.7%)
Using each of these metrics, (with winning percentage as the final tiebreaker) the "Champions" under this analysis are:
ACC:
Wake Forest**
B1G:
Indiana
Big 12:
Iowa State
Pac 12:
Oregon State
SEC:
Vanderbilt
Ultimately, this lines up fairly well compared with overall winning percentage. The only "swap" is Iowa State for Kansas State.
*I broke the tie between Purdue and Minnesota by looking at the better results in the statistic above (conference titles in last 50 years). The Boilermakers edged out the Gophers 1-0, so Purdue was eliminated.
** Wake Forest and Duke tied 1-1-2 in the metrics, but Wake Forest is the ACC "Champion" based on their winning percentage.