Honestly, if you're brand conscious between the big two - it doesn't matter which one you choose as long as you're happy with it.
This boils down to your needs and main reasons why you want a dslr in the first place. Try handling both cameras at the shop - it's important that you are comfortable with the feel, build, and handling of the system.
It goes beyond brands. Having a dslr means - options to play with interchangeable lens. It's important to research the cost of lenses when you feel that you've progress beyond the kit lens. Check out the Canon and Nikon pricelists... are you prepared to pay those prices? How would you feel if you have to pay say $10,000 dollars for a 600mm lens to go with your D90? Pay attention to the economics.
However, if you're open-minded. Other brands like Sony, Pentax, Olympus, Panasonic have decent bodies and a legacy collection of lenses to choose from. Sony has konica and minolta lenses, Pentax has Super Takumars, SMC lenses, Olympus... their ziuko lenses. Many of those lenses are on par, if not better than the current range of Canon/Nikon lenses at "affordable" prices.
That said, there's absolutely nothing wrong if you choose either Canon or Nikon but it is totally wrong if you buy either one and don't even bother to read the owner's manual. In which case, one might as well get a point and shoot camera..... I'm sorry but i have friends who don't even bother to find out how to use a dslr. They only use the auto-mode....
Quite sure, you're NOT one of them.
Good luck on your search. And to all Canon and Nikon users - no offence, yah?