The only one that directly affects RAW is Long Exposure NR, since that takes a dark frame after the exposure and subtracts that from the RAW file before writing it to the card. Note that with Canon, when you set Long Exp NR to off, it really is off (with Nikon, it isn't at least on some models, and there is a median blur filter applied as well, google 'Nikon Mode 3 NR').
The other setting that 'sort of' affects the RAW file is Highlight Tone Priority. This doesn't really modify the RAW data, only the metadata. The camera uses an ISO that's 1 stop less than selected (which is why ISO 100 is unavailable with HTP on), i.e if you select ISO 400, the camera is exposing at ISO 200 (but reporting ISO 400 in the metadata), then it applies a selective tone curve to boost the signal but preserve the highlights. DPP and other RAW converters recognize the HTP flag in the metadata - DPP will apply Canon's tone curve during conversion, other converters will apply their versions. but some converters don't recognize the flag and will just show you an underexposed image.
Do note that NR, color, contrast, saturation, etc., including those settings as applied by a Picture Style, can indirectly affect a RAW image. For a RAW image, the camera generates a JPG preview image that's embedded in the RAW file. That JPG preview is generated using the in-camera settings (picture style, ALO, etc.) even when shooting RAW, it's what is shown on the LCD review, and it's used to generate the histogram. That means if you use the histogram or 'blinkies' (blown highlight alert) to judge exposure, you may expose incorrectly, and that obviously affects the RAW image. You may want to use the Neutral picture style to get a closer approximation of how the RAW file will look, as a basis for the histogram and highlight alert.