I think the original list is pretty good, although it overrates '99 FSU, underrates '05 Texas, and also underrates '02 Ohio State, IMO.
Two facts that tend to get lost in these discussions are that a team's quality is fluid, and upsets can and do happen. The truth is that any of these undefeated teams could have beaten any other of the undefeated teams on any given Saturday....And of course there are teams that were amazing at certain points of the season (i.e. Oklahoma '03) that didn't have the mojo to finish. And then there are injuries - if Willis McGahee didn't go down against OSU, the '02 Hurricanes would probably be in this discussion also as people would debate which of those Cane teams was actually better.
There are many ways to rank them, but there are 3 teams that tend to come out on top consistently - '05 Texas, '04 USC and '01 Miami.
I think an argument can be made that '00 Oklahoma proved the most, and winning 5 games against teams that finished in the top-12 (with 4 on the road) is ultimately a harder achievement than any of the others. Further, the close games were in part result from a wounded QB whose play deteriorated as he battled an elbow injury. Prior to that injury, OU was destroying high quality teams. So one could argue that the '00 Sooner team had the best season.
But ultimately, they fall short because of too many mediocre performances against mediocre teams, and the lack of an elite, balanced offense with a strong running game.
Between the top-3 it is really hard to rank them, and there are all kinds of different arguments for each team.
But this is how I would ultimately bet on them:
1, '01 Miami
This team didn't prove much against elite competition because Nebraska was the only top-10 team they played. If you throw out margin of victories, highlight reels and NFL talent, and just ask yourself, "Who did they have to beat?", their record is nowhere near as impressive as 2000 OU. They had the weakest schedule of the 3 contenders, however they did have a credible schedule with many decent teams, including 6 Sagarin top-30 teams.
I think defense is the most important thing, and their defense was incredible, giving up just 9.4 points per game.. It is worth noting that their rushing defense was not particularly strong, suggesting that Vince Young with '05 Texas might have burned them. But, they did shut down the #1 rushing offense in the country when they had to.
It is hard to look past Miami's '01 defense. Defense wins championships, and Miami's '01 defense was in a different class when it came to keeping other teams from scoring. While their offense didn't put up some of the gaudy stats of others, they were balanced, could run and pass, had the #3 scoring offense, and protected the ball. #1 scoring defense (best of the era) with the #3 scoring offense, and #1 turnover margin (with the best ball hawking defense of the era) results in the #1 spot.
2.'04 USC
'04 USC had some close games against relatively mediocre teams, and their bowl blowout vs. Oklahoma was aided by a bunch of unforced Oklahoma turnovers early. However, their Orange Bowl blowout was the most impressive single game performance, and they had the hardest schedule overall - ranked #7 by Sagarin with 3 top-10 victories and 5 wins over Sagarin top-30 teams.
On paper, there are many reasons why I would rank '05 Texas over '04 USC. The '04 USC offense was not near as potent as '05 because their rushing attack was pretty pedestrian in '04. However, when I analyze the change in USC from '04 to '05 against the Rose Bowl game, it seems that the changes were a big benefit to Texas.
The '05 Texas offense was led by an incredible rushing attack which opened up passing options for defenses that were over matched defending the run. When Vince Young's offenses stalled, it was because because of solid rushing defenses. It was Texas' rushing attack that primarily burned USC in the Rose Bowl, accounting for 8 yards per attempt. This opened up some passing, but it was Texas' ability to run that won the game.
USC's rushing defense was #1 in the country in '04, and fell to #31 in '05. The 2005 Trojans gave up about 50% more yards per rushing attempt than the 2004 Trojans. It isn't just that the 2004 defense was much better (it clearly was), but that it was specifically better at the very skills they needed for dealing with Vince Young. USC's rushing defense in '04 was better than any Vince Young ever faced in college, but in '05 they were pretty mediocre.
On the other side, the USC offense was much better in '05 than in '04 because they had a much more solid rushing attack. However, from a passing perspective, they weren't really any better in '05. The difference between the '04 USC offense and the '05 USC offense is that the '05 version ran the ball much, much better. However, Texas' defense stifled USC's run game fairly well. It was the USC passing game that gave Texas trouble - and Leinart's passing efficiency in '04 was pretty much identical to '05.
Generally speaking, I think improved offense and worse defense is a net negative. And while I don't think USC's improved run game in '05 helped them that much against Texas, I think their gutted rushing defense hurt them bad.
3. Texas
There are many good arguments to put Texas at the top of the list. And in many ways, I think they might matchup better with '01 Miami than with '04 USC.
Texas played two real high quality opponents and won both in nail biters. And they blew out everyone else. However, they ultimately just played 4 top-30 teams, and so they weren't really tested on a consistent basis. Further complicating things is the fact that when they played OU and OSU, both of those teams had inept offenses with green QBs. And in OU's case, Adrian Peterson was out and the offensive line was completely decimated with injuries. That isn't to say Texas wasn't better than OSU or Oklahoma - clearly they were. But it is undeniable that both OU and OSU improved a lot on offense as the season wore on and their relative rank is a result of big improvements in the 2nd half of the season.
Ultimately, it is hard to judge between those 3 teams - but that is how I would bet.