I think this is a much harder question to answer than we think. I've had discussions about this with guys who have watched football for A LOT longer than I have and the only conclusion I can come up with is: I'M REALLY NOT SURE. I wasn't around to watch Rockne's '29 and '30 teams at Notre Dame. I never got to watch the golden domers from '46-49, or Oklahoma in '55 and '56, or Bear Bryant's '64 and '65 teams at 'Bama (even though both teams lost a game), or his late '70's teams. I have been able to see some damn good Miami teams in the '80's (and since then, as well), Nebraska in the '90's, I guess it's USC in the '00's.
Some of us may have seen some of those teams, but I'm not talking highlights, I'm talking about WATCHING these teams week in and week out. I can't look at highlights of Oklahoma's '55 team and determine if they're better than this USC run. I've grown up a Trojan fan, but I hear too many Trojan lovers who don't know what they're talking about say "No way Notre Dame or Alabama or Nebraska could have beaten them". It's like, "OK, well how do you know?" We don't even know who's going to win this year's Rose Bowl, let alone a game between 2 teams from 10 years apart.
Certainly the size and speed of players has improved with time, so we could say that USC would stomp Rockne's teams, but I think the question is who is the best "relative to the competition".
As a Trojan fan who does not want to be biased, I can't take the easy way out and say they're the best ever. Maybe they are, maybe they aren't. One thing I know for sure, they're damn good!