Wow...
Just staying in the SEC: Alabama (pre Saban), Florida (pre and post Meyer), Georgia (the 90's were rough)
Elsewhere, and some of these are still works in progress: USC, Michigan, Penn St, UCLA, Florida St (rebounded now), Miami, Texas, Oklahoma. All of the big elite programs have had down periods that lasted a pretty good while. I mean Alabama who dominates everyone's attention now, absolutely sucked butt for the 90's and 00's.
Nebraska doesn't count ... yet. They have won 9+ games almost every season, they just are no longer mortal locks for National Championships anymore. Someone else said it, and I will reiterate that I would give anything to "suck" that bad. However, with what was one of the most boneheaded hires (I'd say worse than Dooley even), they are quickly going to be longing to "suck" that bad again as well.