GlassDeviant

You can configure Windows to leave Aero in its full glory (if you like that sort of thing) and just edit the properties of the Doom 3.exe file (right click the icon and select Properties). Go to the Compatability tab and tick the checkboxes for "Disable visual themes" and "Disable desktop composition". You may want to do this for TheDarkMod.exe as well, but I don't think that is necessary.