A few other notable mentions, just in the past decade....
L.A. Vs Kings 2002 (this should explain itself)
Spurs vs L.A. 2004 (The .4 shot which at the time was deemed by NBA rule impossible but was still allowed, the rule was changed immediately in the new season)
Spurs Vs Dallas 2006 (Dirk was ushered to the line way to much for a jumpshooter)
Dallas Vs Heat 2006 (Wade was ushered to the line way to much for throwing his body into defenders and flopping)
Spurs vs Suns 2007 (The suspensions, while correct, should have been looked at in context, nothing happened but yet the Suns where severely punished (never say the Spurs dont get breaks from Stern))
Spurs vs L.A. 2008 (the non-call on Fisher, not that I think it would have mattered much, but still.)