Back in 2008 before we left CA I did a little experiment with my XT comparing the noise you have in an image when you get the exposure correct or when you have to adjust the exposure significantly in post processing. I shared it on my photo board but never here. I am going to try to repeat this experiment soon with the 5D mark ii but until then here are the results from the XT version of the experiment.
I started the experiment by metering off my 18% gray lens cloth for correct exposure, then I put a colorful item in the same light (on the cloth) and keeping the aperture the same over and underexposing by 1 stop at ISO 200, 400, 800 and 1600.
Here is an example of the full image
The rest of the images will be 100% crops of a similar part of that image, the info for each image is written on it. All have been corrected back to what the gray card indicated as a correct exposure in Canon's Digital Photo Professional, no sharpening or other post processing besides cropping and adding the text was done.
The 100% crops are not of the focal point, I selected the part of the image that best showed the noise.
I think it is quite clear that you have more noise when you underexpose and bring your exposure up than shooting at that higher ISO and getting the exposure correct in camera. Thoughts?