You typically won't see much noise (if at all) in shadow areas when working with ISO's in the 100-400 range when working with recent Canons. They are excellent peformers in this respect.
I suspect, though, that your problem may stem from underexposing the shot, particularly if you are shooting RAW, and then leaving the 'Auto' settings on popular RAW converters, like Photoshop's ACR. The effect will be to boost the shadows up a stop or two, and it will accentuate the noise enough to be noticeable.
So, the first thing to do is to 'expose to the right' (
Expose Right), as much as possible, without blowing any of the channels (check the R,G,B histogram) in the highlights. Then, when processing the RAW, turn off all the 'auto' functions to start, and then do whatever change you deem needed manually, being careful to not over-boost the shadow areas, lest they erupt in noise again.
If you can't get the exposure high enough, because you are shooting handheld, for instance, then you need to punt and get out the tripod. It's really important to not chronically underexpose a digital sensor, just for the convenience of handholding to get a reasonably sharp image.
The next thing to think about is your lighting. It may be that the shadow areas are indeed just too dark, and if you wish to see detail there, you may need to 'cheat' a little and use some subtle off-camera strobe light (set it on 1/128 power manually, for instance) to add some definition to the shadow areas.
Check out the 'Strobist' blog at
Strobist for some really good info on how to do subtle interior lighting on the cheap, without spending a fortune on lighting equipment.
Hope that helps...
Re: Noise Reduction Software 
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