Can anyone recommend some good noise removal tools, free and commercial? Should support RAW and JPEG. Are certain tools better than others in particular situations? Do some integrate better with other software? Do plugins or stand-alone dedicated NR programs work significantly better than the noise reduction built in to RAW converters?
I think Topaz Denoise and Imagenomic Noiseware are the best. I wrote a thorough review on the previous Topaz Denoise (It's in Hebrew, yet Google Translation makes it readable and understandable in English). It should be even better now (Version 4).
I use Noise Ninja. I don't have any experience with the other so I'm not sure how to compare it, but it did seem relatively easy to use, albeit a little overwhelming in terms of features and controls offered. I think the home standalone is around $35. You can buy plug in versions for photoshop, etc as well.
Here's a link to the User Manual for version 3.12 of Canon's Digital Photo Professional.
(I don't yet have enough reputation to add comments to someone else' answer.)
Noise removal tools are mostly based on the wavelet denoise technique.
You can get a good wavelet denoise plugin for Gimp
Gimp wavelt denoise plugin
This allows you to independently adjust noise reduction in the Y, Cb and Cr channels
well this answer maybe too late since the question was asked from almost a year but for the sake of others who will search this website looking for a noise removal tool, I do really recommend Noiseware from Imagenomic. In my opinion, it's the best noise removal tool so far and it doesn't degrade the photo sharpness a lot. It's in version 5 now.
Another late answer. I find the noise adjuster in Capture NX2 very good, so I should imagine that the same company's Dfine 2.0 would be worth a free 15 day trial. It allows you to apply noise reduction where you want it which makes it easy to eliminate noise in your some areas of your images while maintaining detail and sharpness overall.
If you shoot Canon, their "Digital Photo Professional" software that comes with the cameras actually has a pretty decent noise removal tool.
I recently purchased Nik Dfine 2.0 and I am really impressed with the results. It does a really good job of removing noise while still keeping sharp details in the image. It performs extremely much better than the noise reduction in Aperture 3.
You can get it as a plugin for Photoshop, Lightroom, and Aperture. There is a 15 day trial so you can try it out.