Bonusweb got a reponse from John Carmack regarding GeForce FX performance in Half-Life 2 & expected performance in other future games (Doom III namely).

Unfortunately, it will probably be representative of most DX9 games. Doom has a custom back end that uses the lower precisions on the GF-FX, but when you run it with standard fragment programs just like ATI, it is a lot slower.

Would you like to know more? (http://english.bonusweb.cz/interviews/carmackgfx.html)