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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?

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It's effective. Basically, the camera can use the second, dark frame, to subtract signal out of the first frame, so it definitely gets used in RAW. In fact, if you try it, you'll discover that you end up with only one RAW image as the DFS image is discarded after use.

On this topic, however, I'd note that you want to use this carefully. If you're doing long night exposures, DFS can double the amount of time it takes to snap a shot and that cuts into your shooting time. Many astrophotographers will do their own DFS after the fact as a result of that and us Pentaxians are gnashing our teeth because we have no option to shut it off (my only complaint about Pentax).

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    \$\begingroup\$ +1: Great point about astrophotography...it really hangs you out to dry when your trying to get nice sky shots on those rare, fully dark nights. \$\endgroup\$
    – jrista
    Commented Aug 21, 2010 at 0:03
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    \$\begingroup\$ @jrista I got bit by it once doing by doing a one hour exposure trying for star trails... Fortunately my battery was fully charged. \$\endgroup\$
    – Joanne C
    Commented Aug 21, 2010 at 0:46
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    \$\begingroup\$ Not sure if its the same on the Pentax, but if I just switch my Canon off during dark-frame capture I'm pretty sure (its been a long time since I've left dark-frame subtraction on ;) it writes the file to the flash (presumably ditching the dark frame subtraction). So could be worth trying it out to see if you can manually skip the dark frame on particular shots? \$\endgroup\$
    – drfrogsplat
    Commented Aug 22, 2010 at 2:11
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    \$\begingroup\$ @drfrogsplat, on my Canon 350D, if I switch it off while it's dark-framing, it'll finish the dark frame and then switch it off. Which is okay if it's the last shot, since I can just put it back in the camera bag, and let it do it's thing while I head to bed. \$\endgroup\$
    – Conor Boyd
    Commented Aug 22, 2010 at 20:45
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    \$\begingroup\$ I have found that exposures longer than 1 min (without the dark frame subtraction) with my 5D & 5DII exhibit noise that sort of looks like grains of rice. Using a variety of noise reduction software I've found them difficult to eliminate. The dark frame subtraction seems to work much better. Interestingly my old 20D is much cleaner with long, night time exposures, even with the NR turned off. \$\endgroup\$
    – Henry Peach
    Commented Aug 23, 2010 at 13:24
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Yes, the long exposure noise reduction is applied to the RAW file also.

Regular noise reduction is not done on the RAW data. As that only uses the data in the image, it can be repeated afterwards. The long exposure noise reduction uses the data from another exposure to correct the data, so that can't be repeated from only the RAW data.

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Can you test it out? Take a picture with noise reduction off, then with noise reduction on, and then you'll see.

As you said, it's probably a dark frame subtraction, meaning that any bias patterns that are present in the chip will get removed. These bias patterns show up on longer exposures, as in, some pixels may be more sensitive than others, so the dark frame will identify those inter-pixel biases and allow the camera to correct them. That means that it should affect RAW frames, because the intensity information from the dark frame will still be removed.

I know that it worked on my D70 back when I took pictures of the night sky. It's harder for me to find a region without light pollution nowadays.

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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: alt text

Canon DPP (noise reduction disabled): alt text

Adobe Camera RAW (noise reduction disabled): alt text

Adobe Camera RAW + Topaz Denoise (RAW-moderate setting): alt text

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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    \$\begingroup\$ Its very hard to see...perhaps a long shot of something around 18% gray would be better? \$\endgroup\$
    – jrista
    Commented Aug 21, 2010 at 23:53
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    \$\begingroup\$ JPEG has additional processing applied which, I think, you haven't matched. One obvious one is noise reduction, other than with Topaz, but you cannot assume that Topaz is doing the same thing as the camera. In fact, Topaz has created a more even appearance which I would expect from a black cap shot. Also, DFS isn't perfect, heat effects noise and the second exposure will be hotter than the first. \$\endgroup\$
    – Joanne C
    Commented Aug 22, 2010 at 2:23
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    \$\begingroup\$ @Karel That's not a criticism, it's just an explanation for what you saw. For the record, I agree with you on using DFS and if I had the option to shut it off in my camera, I would. It works, but is not perfect, and doubles your shooting time. \$\endgroup\$
    – Joanne C
    Commented Aug 23, 2010 at 10:45
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    \$\begingroup\$ Do you have a 'control' set, with the same exposure time and post-processing techniques, but with long exposure noise reduction turned off? \$\endgroup\$
    – Evan Krall
    Commented Aug 26, 2010 at 20:54
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    \$\begingroup\$ Not to mention that it is hard to measure a Signal to Noise Ratio when the lens cap is allowing ZERO SIGNAL to reach the sensor. \$\endgroup\$
    – Michael C
    Commented Oct 12, 2013 at 19:14
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I've found that when using a Tv between 1 and 30 seconds or so it is quite effective. Once I process in DPP I am able to use less NR and save more detail. The subtraction is done to the RAW file, but that doesn't mean all the noise will be eliminated, only that caused by bias patterns in the chip. Other sources of noise, such as shot noise, will still require NR in post.

I don't have the patience to try it at longer than 30 second exposures.

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