All 4 les have asterisks:
1999* -- shortened season
The aging Spurs benefitted from not having to survive the long grind of an 82-game season. What in most years would have been a late regular-season peak turned into a playoff run. The distortion imposed on the season by the abbreviated schedule is readily shown by how the eighth-seeded Knicks won the East. The Spurs themselves distorted the game by exploiting all the loopholes in the defensive rules to turn what once was a fluid, beautiful, high-scoring sport into a bunch of 75-70 wrestling contests. The league had to change the rules just to keep the Spurs from killing the game.
While the 1999 season certainly shouldn't be swept from the record books, it always should be noted that the cir stances of the season were totally different from a normal season, and so the 1999 championship is different from all the others.
2003* -- Dirk Nowitzki and Chris Webber injured
The Sacramento Kings, at or near their peak, lost this season when Chris Webber blew his knee out in the playoffs. Then the Dallas Mavericks lost Dirk Nowitzki. The Spurs yet struggled to put the shorthanded Mavs away. It is very doubtful given what happened, and given how Nowitzki has given the Spurs fits since, that the Spurs could have prevailed with a healthy Dirk available.
2005* -- Joe Johnson injured
Joe Johnson was lost to an eye injury for Games 1 and 2, and was still limited upon his return. Nevertheless, the Suns still managed to take one game in San Antonio with him in the lineup, making it clear that it would have been an entirely different series with him at full strength. His career in Atlanta since then only underscores the difference he would have made.
2007* -- Amare Stoudemire and Boris Diaw suspended
This was one of the most ignominous episodes in NBA history, when the Spurs were rewarded for underhanded, dirty play on a technicality. The Suns clearly were going to win that series until two of their best players were suspended a game for coming off the bench after Robert Horry brazenly slammed Steve Nash into the scorer's table in frustration after losing Game 4. The Suns still nearly managed to take Game 5 but simply didn't have the legs to close it out shorthanded. Making it worse was that video after the fact showed that Tim Duncan himself had come of the bench earlier in Game 4 after a Spur fell to the floor, yet he was not suspended.
Once the Tim Donaghy scandal exploded, it was revealed that other Spurs playoff victories may have been fixed. Really, the NBA ought to just vacate the 2007 championship given all the questions surrounding its validity.
So really all four of the Spurs les are tainted. What they are going to be remembered for is being a team which didn't really respect the NBA game, playing a boring style with no regard for entertainment, winning flukish championship through brutish thuggery during an time when there was no dominant team and all the true contenders suffered freakish bouts of bad luck. Their "reign" will simply be the proof that the middle of the aughts was a dark time in NBA history.