I'm experimenting with some noise reduction, with an algorithm along these lines:
http://www.computersdontsee.net/index.php/post/2013/02/09/Introducing-NL-meanshttp://bengal.missouri.edu/~kes25c/nl2.pdfhttp://scholar.harvard.edu/files/stanleychan/files/chan_zickler_lu_2013_0.pdfhttp://www.cs.tut.fi/~foi/3D-DFT/ - watch the animation


According to the logs, this squeezes roughly one more stop of dynamic range, and it seems to whiten the noise too.
Download:
cr2hdr-denoice.exeThe denoising step is not enabled by default; you need to specify --denoice in the command line.
Now the big question: how does this compare with state-of-art denoising software? (Lightroom, Neat Image, Noise Ninja, whatever you use). I don't have license for any of these, so I don't know if I'm reinventing the wheel or not.
For comparison, I suggest processing the CR2 with default options, then with --denoice, then postprocessing both DNGs in your favorite editor and denoise them so they have similar noise levels, and see which one holds more detail. Your quest is to find out whether my denoising step helps or hurts, and how much.
Original CR2 files for these examples:
7O4C8804.CR2,
6X8A0381.CR2 and
IMG_5762.CR2 (credits: AdamTheBoy, daancalo2013 and Danne). To get the DNGs from the top row, process them with default settingss, and to get the DNGs from the bottom row, process them with --denoice.
Please note that each test run will create a different DNG (the denoising algorithm uses monte carlo sampling). It may be interesting to see what happens if you average the output from a few test runs (didn't try). Also it may be worth trying --denoice --cs5x5.