I was just about to start a new thread almost exactly like this one.
Weird.
I was wondering what are the pros and cons of the Nikon and Canons?
They seem to be almost as controversial as the Mac vs PC thing.
Why would you choose one over the other?
Pros: They're the market leaders.
Cons: They're priced and featured like market leaders.
Short answer: If you're not going to be buying lenses that are over the $1500 range, then mostly go based upon what feels better in your hands. If you're going to be getting anything better than the Canon 100-400IS or Nikkor 80-400VR, then you need to look at what you're going to shoot, the lens line, flash systems and all the associated stuff. If you're going to shoot weddings, pro sports, or sports for money, then you'll have a lot more criteria.
At the low end, Nikon's currently kicking Canon's butt, and at the high end Canon's currently kicking Nikon's butt. Both companies offer bodies at both ends, and can mostly satisfy their respective customers at both ends, so image-quality-wise anyone who doesn't do billboards for a living isn't going to really make any signiciantly different images with either camera system.
It's a system though- once you start spending real money it's a pain in the butt to switch (though more and more folks seem to be ending up with bodies from both systems, and an unnervingly large sampling of "pro" photographers seem to be switching back and forth (quotes for emphasis- just because you make money with a camera doesn't make you a good photographer.)
In my experince, about 65% of folks prefer how Nikons handle and about 35% prefer how Canons handle, even though there's a large variation in body sizes and weights in each system. Canon's current lens line is a little better than Nikon's at the pro end, and I think a little worse at the pro-sumer end. Nikon's flash system tends to be a bit better, both systems do well with metering.
In the end though, it's really about the pictures, and even a marginally good photographer can get great results out of any current body from either manufacturer (and most of the other manufacturer's DSLRs too.) Look at your budget, decide which models fit there (especially with lenses- that's where you spend your long-term money anyway) and then if you live somewhere that has a camera store or retailer with those modles, go try them out. Avoid camera store salesween bias if you can, just take some snaps with your favorites, and see what the results are like, then make your choice.