RAW files on the other hand will naturally not have any in-camera noise reduction applied and it will be up to you to determine if and how much will be applied during post production. You will likely be able to notice noise even at and ISO as low as 200 when viewing your RAW files at 100%. If not removed, that noise will be present in the exported JPG as well.
When working with Darktable, there has been a profiled noise reduction option since version 1.2. As the name implies, the Profiled Denoise option is based on unique camera model/ISO combinations to optimize the noise reduction while retaining image quality. From working with my RAW files I have found this to be a fantastic option that works very well and it is usually the first edit I apply to any of my images.
For comparison, here is a series of 100% crops taken at ISO 200, 800, 1600, 3200 & 6400 with the Darktable edited photo on top, and the straight off the camera photos on the bottom. The color difference is simply the difference between the standard setting on my Nikon D5100 and the RAW image after Darktable applies it's built in base curve. The Profiled Denoise was set to the default value on all images except for the ISO6400 shot, which was changed to patch size 3, strength 3.
For reference and more in depth comparision, you can see all the full resolution shots at this Flickr Set.
I have found working at ISO400 gives me a good balance between low initial noise, quicker shutter speeds and very little detail loss from the denoise algorithm. Below is a good example of a developed photo taken at ISO 400: My Father-in-law's 1964 Impala SS.