I think saying that any company has the best DooM 3 GPU is premature at this point. By the time DooM comes out there will be a whole NEW set of video cards, and depending on the relative performance gain, either company could end up with the best DooM 3 video card.
Wouldn't it be embarrasing to Id Software if shortly before DooM 3 is released, ATI's new card comes out and outperforms nVidia's new card in DooM 3 by 50%? Don't laugh, it could happen; just look at how slow nVidia cards run Half-Life 2 at present.
EDIT: Oh yeah, and Alienware chooses the video card for their laptops by what is the fastest available at the time. And guess what? The Radeon 9600 Pro mobility is faster than any of the current nVidia solutions. So Alienware chose it.
Alienware has put nVidia chipsets into the a51m before, when they were the fastest. In the future they might do it again if they're the fastest again. But for the short term, ATI's got the mobile game in the bag; Alienware is upgrading to the Radeon 9700 Mobility, not an nVidia part.