I am not sure what first to use in the work flow: Noise Ninja and then all other adjustments?
There reason I am confused is that Noise Ninja also does sharpening , but usually sharpening is recommended as the last editing step.

vphoto

The very first thing I do after RAW conversion is use Noise Ninja. I use it on every shot - even the ones shot at ISO 50. It's a very flexible and easy-to-use program.

Use Noise Ninja to remove noise, not for sharpening or anything else. It really shines when you use it on separate layers so that you can fine tune the noise reduction on different parts of your image (e.g. strong for shadow areas and sky, weak for faces, ...).

I guess the answer depends upon which RAW converter you use. I use DxO Optics pro and although their default noise reduction is way too much, I have a preset that does very slightly apply noise reduction as part of RAW conversion.

But I would still say that if you find large areas of your ISO 100 shots need Noise Ninja, you should look at what's wrong with the expsoure.

Images from point and shoots at high ISO are typicallly very noisy, but Canon and Nikon DSLRs at low ISO with proper exposure are generally fine unless there's a very deep shadow area somewhere or the image is underexposed.

Noise Ninja is a great tool, but you will remove detail when you use it, so it's important to do so only when necessary.