1. Alabama
No program has won games and championships as consistently over time. Top 5 all-time wins and win percentage. Unsurpassed in national titles (save for #10). Claims NT's in every decade from the 1920's on except for the '50's and 80's.
2. USC
Could interchange with #3 or #4, but I favor consistency in championships slightly over consistency in wins.
3. Notre Dame
Some want to use recency bias against them despite the fact they remain relevant, playing in one BCSNCG and the playoff last year. There are few who can measure up to Alabama over time and until CNS came along this program was arguably number one all-time. The trend is downward, but that doesn't remove history. The recent dirth of championships compared to #2 does take them further down the list than I expected.
4. Michigan
Number one in all-time wins and the same number of titles as numbers 2-3, but titles are front-loaded. Hard to believe 49 years passed between their next to last and last title, with the last being 22 years ago. Could easily put Ohio St here, but this is all-time and not all-recent.
5. Ohio St
Later start to their greatness than Michigan and if based on the last 70 years only would easily outrank their hated rival. hmmmmmm...(sorry, couldn't resist)
6. Oklahoma
fact: 4 teams have as many or more titles than OU -Princeton, Yale, Pitt (what?! It's true, though), and Harvard - but Pitt is the only one to be relevant in the last 60-80 years with its last title in 1976 and falling a little short in 1981. That said, OU has been more consistent and is still quite relevant while the others aren't really even in the picture any more.
7. Nebraska
Similar resume to #8, but one more title tips the balance.
8. Texas
#4 in terms of wins, but only 4 titles.
9. Tennessee
More titles than #7-8, and though still top 10 in wins they lag far behind the Cornhuskers and Longhorns in wins and win percentage.
10. Tie: Princeton/Yale
No, they aren't relevant today but are still more deserving of a mention here than others based on a number of factors. This is an all-time list, after all. These were the early powerhouses of college football and paved the way for others. Several others have been more relevant of late, but they have their own deficiencies in terms of wins, winning percentage, number of titles, and consistency (not to mention sportsmanship and moral fortitude). The pickings are really slim by this point, so why not honor the two teams with more titles together than the next 4 teams behind them including Alabama, ND, UM, and USC?