There have been 11 BCS championships so far in the BCS era, and a fan's mind cannot help but want to compare great teams across years.
As a result of my own curiosity and desire to answer these types of questions, I have made a list of the top 10 teams in the BCS era—though not all of them were BCS champs (it is a simple fact that in some years, the level of play was just better than in others).
I will go in order from best to last, so there will be no suspense as to who I think is the best team.
1. 2001 Miami Hurricanes
I know, I know, not creative because everyone says this is the best team of all time. But can you argue with them? With a lineup featuring first-round draft picks such as Bryant McKinnie, Andre Johnson, Jeremy Shockey, Ed Reed, Jonathan Vilma, D.J. Williams, Jerome McDougle, William Joseph, Mike Rumph, Phillip Buchanon, and RBs like second-round pick Clinton Portis (whose backups were Willis McGahee and Frank Gore), this was practically an NFL team, especially on defense.
Factor in a few late-round picks here and there and you've got a team almost completely filled with NFL players; these guys played like it too, absolutely dominating everyone they played.
2. 2005 Texas Longhorns
This team played the toughest opponent of any team on this list in the national title game, winning an epic Rose Bowl over the 2005 Trojans. Vince Young was magnificent throughout the season, guiding comeback victory after comeback victory, performing under huge pressure (4th-and-18 vs. Kansas) and repeating it on the big stage (4th-and-5, 19 seconds left, national championship on the line).
Forget about Tim Tebow and Matt Leinart—no QB performed better and delivered more under pressure or in big situations as Vince Young did in 2005.
He had a great team around him too, including players like Limas Sweed, and Michael Huff on defense (before he sucked it up in the NFL, he was an All-American and the reason VY was able to work his last second heroics; he made the 4th-and-1 stop against LenDale White and USC to get Texas the ball again), among many others.
3. 2004 USC Trojans
This team was offensively stacked, with Heisman winner Matt Leinart, Reggie Bush, LenDale White, Dwayne Jarrett, Steve Smith, and Dominique Byrd, and the defense, while it lacked many big name players, was solid and able to keep games low-scoring (only allowing 20 points or more on three occasions, and never more than 28).
In addition, this defense absolutely dominated former Heisman winner Jason White, Adrian Peterson and Oklahoma in the national championship game, allowing 10 points before some fourth quarter garbage time production after USC went up 55-10 gave OU 19 (and two of those were on a safety).
Though it did not score as much as its successor (2005 USC), this team was able to win with solid defense (unlike '05 USC) and not rely on its star-studded offense to guide it through shootouts.
As a result, I really think this team and the 2005 Longhorns' spots are interchangeable, but the '05 Longhorns got the nod because well, they beat USC a year later.
4. 2004 Auburn Tigers
These guys didn't even get to play in the BCS title game, and that was a ridiculous slight (though if they had played in it, undefeated OU would have cried foul). However, I can guarantee this team was better than the OU team that was fed to USC.
Auburn traditionally has had great defensive teams, and this may have been one of the best of them all; a speedy, hard-hitting defense kept opponents in check the whole season, but the offense is what distinguished this Auburn team from others. This offense was actually competent.
Actually, it was more than competent—it was good. Though it did not light up scoreboards and was relatively boring to watch, it was a strong power running game, featuring RBs Ronnie Brown and Carnell "Cadillac" Williams, who would become the second and fifth overall picks in the 2005 NFL draft.
They could pass too (Auburn can pass?); for once they had a good QB in first-round draft pick Jason Campbell. While I don't think they would have beaten USC had they played, I definitely think this team at least deserved the shot; keep in mind they ran through the SEC undefeated, with their only close game being a 10-9 victory over reigning BCS champs LSU).
5. 2008 USC Trojans
This is the best team with a loss, and I know Florida fans would scoff at this ("We won the BCS champ, you beat PSU"), but just look at sheer talent. An absolutely unbelievable defense, featuring Brian Cushing, Clay Matthews, Rey Maualuga, Taylor Mays, Fili Moala, Kaluka Maiava, Cary Harris, and Josh Pinkard simply refused to let other teams score (except for that one ultra-publicized quarter against Oregon State).
Combine that with an absolutely loaded offense featuring Mark Sanchez, Damien Williams, Patrick Turner, Joe McKnight, C.J. Gable, Stafon Johnson, and a crop of future NFL linemen, and you have an amazing team.
I really think this team is the most talented USC team of all, and could beat the 2004 version, but the fact remains that they did lose one game, so that keeps them out of the top four. In a few years, check some drafts and see how high most of this team went; it is like a somewhat toned down version of the '01 Canes.
6. 2008 Florida Gators
Tim Tebow is God, your life is better for spending five minutes around him, he has graced college football by allowing us to witness his greatness, etc. Really though, he is a great player and leader, though I believe there was a better player on his team.
Percy Harvin was Florida's Reggie Bush this year, and though often injured, he was crucial in most of Florida's victories.
After the loss to Ole Miss and Tebow's subsequent (and ridiculously publicized) speech, they made good on their word and dismantled everyone, until Alabama and Oklahoma, and came out with solid, convincing victories in those. It's a shame that they couldn't play USC, because that would have been a matchup for the ages.
However, I put USC on top because of their NFL talent—Florida's gimmicky offense would have some trouble going against an NFL-caliber defense.
7. 2005 USC Trojans
This team had an amazing offense, with two Heisman winners in the same backfield. It returned all those offensive players from the 2004 team, but lost some defensive talent, and allowed some teams to score lots of points.
Eventually, this over-reliance on offensive firepower came up short in the three-point loss to Texas.
But offense can't get you everything, and I think that this team would have had a bit more difficulty than usual if it faced the defenses on the teams listed above it here, and as such I put them at seven; call them a better version of the 2008 Oklahoma Sooners (yes, I know the Sooners scored more, but they went against Big 12 defenses and gleefully ran up the score; 60 points is almost never necessary, not to mention a 57 point effort against Chattanooga).
8. 2002 Ohio State Buckeyes
This team was the least impressive national champion of them all. Its offense was disgustingly mediocre, though Maurice Clarett was impressive, and its defense was strong, but never strong enough to really fully compensate for that anemic offense.
All the teams above this team dominated most opponents; this team had close, nail-bitiing encounters with almost every single Big Ten also-ran.
Though they got out of it undefeated and unscathed, there was an overall lack of impressiveness in their wins which transcended the lack of style points; you just knew they weren't much better than their opponents..
However, the fact remains that they always found a way to win, and beat a 2002 Miami Hurricanes team, which was absolutely stacked with NFL talent and first round draft picks (though a very controversial pass interference call in overtime stopped the Canes from pulling out of this one unbeaten).
Nevertheless, winners are winners, and this team was one of them.
9. 2002 Miami Hurricanes
For some reason, this team never gets the respect it deserves (probably because they lost to the aforementioned Ohio State team which gets no respect for the reasons outlined above). But this team was almost as dominant as the '01 version, and NFL talent was abundant on this roster; where players like Ed Reed left, Sean Taylor filled in.
In reality, they had the NFL talent to beat almost any team out there, but their coaching was poor; their wins were purely a result of unbelievable talent. When they met their match in talent (Buckeyes, almost all of whom were drafted at some point), albeit horrifically under-performing talent, they lost.
Funnily enough, for all those Buckeyes who were drafted, not a single one of them has made a single Pro Bowl, so I guess that talent underperformed at the next level too. Still, the '02 Canes were an awesome team.
I cannot think of one team that stands out from the rest and deserves this spot, so I am going to leave it blank.
You will notice that no team from 1998 through 2000 made this list, despite those champions going undefeated—this is intentional because I believe that the quality of football then was not as high and the risk of upsets much lower than it has become in recent years (what with the advent of the spread, general advancement of the game, and talented recruits deciding to play and become stars at non-powerhouse schools instead of sitting on powerhouse benches).
In addition, the 2000 season had a disgusting BCS slight, with Florida State getting to play Oklahoma despite losing to a one-loss Miami team with the same record as them going into the NCG.
In fact, yet another team was slighted, and never really even is thought of as having suffered an injustice; I refer to the Washington Huskies, who also lost only one game to a strong Oregon team, but managed to hand the 'Canes their only loss of the season. As a result, I think Oklahoma got a far easier opponent than they should have in the NCG, and as such, do not value their victory as much.
So this is my list, and feel free to comment, question my ordering, or even call me an idiot for leaving off whichever team you feel was better than those I listed.