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As mentioned above, Nikon cameras do postprocessing of the "raw" images. This can be overcome by switching off the camera during postprocessing.
Until recently the main difference was that Canon used CMOS technology while Nikon was using CCDs (made by Sony). Canon generally had lower amp glow which made them more popular for astrophotography. However, some newer Nikon's are also CMOS based and I am not sure how they would compare.
And of course, some Nikon models are better than the others, for example quite a few people are using D40 for astrophotography.
For daytime photography, there is not much difference though.
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