Play around with both and see how you feel about the user interfaces of each.
I'm not certain about specific features and recent advances, but I am under the understanding that the difference is similar to the Coke vs. Pepsi hype: it boils down to preference.
That said, I am quite pleased with my Nikon D40, with the exception of it not having the a manual focusing grain/ring in the viewfinder. I'm not certain that even exists in the modern camera market.
Also: look into the Sony DSLRs, I can't tell you much about them except that a couple of my friends swear by them.
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