I can configure my camera (5D) to use long exposure noise reduction (dark frame is exposed and subtracted), but is this method really effective when shooting RAW? Or is the actual subtraction only done when shooting JPEG?
Answer
Wasn't really intended this way (and I didn't have this information when I asked the question), but my experience shows different results. I made a 556-second exposure at ISO 400 with lens cap on and long exposure noise reduction switched on and RAW+JPEG configured. The results are 100% crops with no additional processing applied.
In-camera JPEG: 
Canon DPP (noise reduction disabled): 
Adobe Camera RAW (noise reduction disabled): 
Adobe Camera RAW + Topaz Denoise (RAW-moderate setting): 
My conclusion is that there is no point shooting only RAW with long exposure noise reduction on (expose and subtract dark frame) as it doubles exposure time and its effect is questionable unless done by the camera.
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