In the decade of the 2000s, the winningest teams:
1 Boise 112-17
2 Texas 110-19
3 Oklahoma 110-24
4 Ohio St. 102-25
5 USC 88-25 (after vacated wins)
6 Florida 100-30
7 TCU 95-29
8 LSU 99-31
9 UGA 98-31
10VT 99-32

These were the only teams winning 75% of their games. Boise, TCU, Georgia and Virginia Tech never played in the BCS title game in that decade. Texas played twice, winning one and losing their QB in the first series in the other game. Oklahoma only won one, although they lost 3 times. Ohio St. only won one (when they were a huge underdog), although they lost two times as favorites. USC only got there twice, winning one and losing one. Florida did win twice, barely getting in the first time. LSU did win twice, once after an upset win in the SEC title game and once with 2 losses when everybody and their dog lost the last weekend.

That's 8 of the 10 titles and 7 of the runnerups (Miami and Alabama won the others while FSU, Nebraska and Miami were the other losers), but no more than 2 titles per team and 4 never even got to play for it.