In a message there, Carmack said that the NV30 technology is slightly faster on most Doom scenes, but sometimes the R300 technology pulls ahead.
It's complicated, he said, because of the different way cards using these graphics chips run the game.
He said that NV30 runs Doom in five different modes, while the R300 runs the game in three different modes.
Using an apples-to-apples comparison makes it look as if the R300 is twice as fast, but using vendor specific paths gives the NV30 GPU a clear advantage.
He also says that taking up two slots is a disadvantage for a GeForce FX and the cooling fans are VERY LOUD (his caps).
You can find all of his comments, here. ยต