I know this is too general question, but I'll give it a try..
About an hour research in photo.SE, I found some question, that are related to this one:
Does the camera white balance setting affect the raw image at all? - short answer - NO
Why is Aperture changing the color of my RAW photos? - no short answer :D
Does "long exposure noise reduction" option make any difference when shooting RAW? - short answer - YES
Is in-camera high-ISO noise reduction worthwhile? - one more about noise reduction
Do different "Picture styles" affect RAW output? - short answer - NO
Shutter speed and aperture are obvious, of course.
What other settings may affect a RAW photo?