That legacy was tarnished Thursday, and Carroll, Bush and many other ex-Trojans aren't happy about it.
The NCAA threw the book at the USC football program, giving it a two-year postseason ban and four years' probation, taking away 30 scholarships over a three-year span and forcing forfeits of an entire year's games for what it deemed improper benefits given to Bush from 2004 to 2005.
More sanctions might be coming, too. Bowl Championship Series executive director Bill Hancock said in a statement that the organization's presidential oversight committee will soon meet to discuss whether USC will be stripped of its 2004 title. Hancock said there would be no 2004 BCS champion if USC's victory is vacated.
The developments left Carroll, who departed USC for Seattle in January, "absolutely shocked and disappointed."
"I never ever thought it would come to this," Carroll said in a video statement posted on YouTube. "After nine years of working at the university and going through all of the challenges and accomplishments that all of the people took part in, I'm extremely disappointed that we have to deal with this right now. I never thought there was any facts that supported these significant sanctions that have come forth.
"The primary issue during the process was, did the university know? The university didn't know, we didn't know. We were not aware of any of these findings."
Carroll went 97-19 in nine seasons at USC, a run during which he won seven consecutive Pac-10 titles and two national championships. One of his stars was Bush, who claimed the 2005 Heisman Trophy as college football's best player, then was drafted second overall by the New Orleans Saints, with whom he still plays.
But the NCAA said in its report that, while at USC, Bush received lavish gifts from two fledgling sports marketers who hoped to sign him. The men paid for everything from hotel stays and a rent-free home where Bush's family apparently lived to a limousine and a new suit when he accepted the Heisman in New York in December 2005.
The NCAA found that Bush, identified as a "former football student-athlete," was ineligible beginning at least by December 2004, a ruling that could open discussion on the revocation of the Heisman. Members of the Heisman Trust have said they might review Bush's award if he was ruled ineligible by the NCAA.
The NCAA also wants USC to vacate 14 victories in which Bush played from December 2004 through the 2005 season. USC beat Oklahoma in the BCS championship game on Jan. 4, 2005, and won 12 games in the 2005 season, which ended with a loss to Texas in the 2006 BCS title game.
Bush released a statement voicing his objection to the NCAA's ruling before it was officially announced.
"I have a great love for the University of Southern California and I very much regret the turn that this matter has taken, not only for USC, but for the fans and players," Bush said. "I am disappointed by (Thursday's) decision and disagree with the NCAA's findings. If the University decides to appeal, I will continue to cooperate with the NCAA and USC, as I did during the investigation. In the meantime, I will continue to focus on making a positive impact for the University and for the community where I live."
USC later said it plans to appeal some of the penalties that it deems excessive. A resolution of any appeal isn't expected until next spring at the earliest.
"I take the same stance as our university," said Lane Kiffin, the former Oakland Raiders coach who took over for Carroll. "There is some guilt, but the punishment is too severe. That's why the appeal process is taking place."
Sixty-three former USC players are currently on NFL rosters, so as word of the NCAA's ruling spread, the chatter in locker rooms and Web sites increased.
Shaun Cody, a Houston Texans defensive tackle and member of that 2004 USC title team, seemed to brush off the sanctions.
"I think it's a bit steep, to be honest," Cody told the Texans' official Web site. "I still beat Oklahoma (55-19) in the national championship game, so I really don't care all that much.
"For the guys who weren't doing anything, I think it's pretty harsh and pretty silly. But it's not like I'm worried about it. I know what I did in my career there. I'm sure everyone knows what they did. So it's not that big a deal."
Another Texan, offensive assistant Bruce Matthews, has deep ties to the school. Matthews was an All-American lineman at USC, and his brother, Clay Jr., and his nephew, Clay III, also played there.
"That was a great run in 'SC history, but unfortunately, the actions of a few spoiled it for the other guys," Matthews said. "I think 'SC does it the right way. Unfortunately, in this case you've got a lot of guys paying for the sins of just a few individuals or who knows how many guys.
"One of the best things about a team sport is you share in the accomplishments as a team, but unfortunately when one guy screws up, you all can pay the price, the whole team can pay the price. That's unfortunate."
Clay Matthews III was the target of some good-natured teasing by one of his Green Bay Packers teammates. Aaron Rodgers, who played at quarterback for second-place California in 2004, took to Twitter to thank Matthews for helping him receive some championship hardware.
"Looking forward to getting my PAC-10 championship ring from the '04 season," Rodgers wrote. "Thanks @claymatthews52."
Matthews laughed off Rodgers' message, saying, "I love this dude @AaronRodgers12!! Quietly emerging as 1 of the most outspoken QB's in the NFL... That's my quarterback *T.O. cry*"
Bruce Matthews knows USC haters are enjoying the Trojans' fall from grace, but he had a warning.
"The tradition's been going on for a long time there, and I think the type of guys that go there are aware of that," Matthews said. "It's just one more thing to overcome. Like I say to all the other coaches here when I talk about 'SC, when you're on top, everybody's shooting for you. So enjoy it. We'll be back."
Carroll echoed those sentiments.
"I feel terrible for the Trojan family that we have to go through this," the coach said. "But, as always, we'll be strong and we'll keep our heads up and we'll keep fighting on. I'll continue to support and cooperate, again, the appeal process and do everything I can to help. Fight on."
The Associated Press contributed to this report.