It's interesting that you can play Quake 4 but not Doom 3 since they use the same games engine and are almost identical in appearance.
In fact being newer Quake 4 has some advancements on Doom 3 and is a bit more graphically demanding.
My first thaought is that the card is overheating.I'm assuming that it is not overclocked in any way.
Are their any differences in the settings you run Quake 4 and Doom 3 at?
Is there good air flow through the pc case......no vents blocked with fluff etc and are all the case fans working correctly?
Try temporarily taking the pc case side off and see if the problem persists.
If you haven't already done this you could try reinstalling Doom 3 or one of the other games that doesn't run.