I personally shoot Canon at the moment because it was a cheaper alternative for me. I simply couldn't find a cheap D50 to replace my broken one. I only use my sigma 30mm f1.4, so I figured sell my Nikon mount to get a Canon one. However, I still haven't sold my nikon mount 30mm, or my SB-600. If the D90 can give some of the high ISO quality of the D300(I'll settle for less FPS and AF points/tracking), I'll sell my 350D setup and go back with the D90. Yeah canon's 40D successor will be out, but I'm sure it won't be in my budget. Here's some deciding factors that I'd go over:
Ergonomics: Simply opinion, but I like how Nikon's hold in my hand compared to Canon, especially at consumer levels. They fit my hands better. A Canon with a grip helps tremendously though, and is probably why I've been able to stand this past month with one. To be fair, my aunt's 5D fits like a glove, despite me not feeling at home with the controls. I also disliked taking my trigger finger off the shutter to adjust shutter speed/aperture with the rebels. I preferred using my thumb, that way I can still refocus(say following someone on stage) while adjusting settings.
Bodies/sensors?: I think both groups can agree that Canon bodies are noticibley sharper, where as Nikon's handle noise better. A lot of people think Nikon's noise reduction hurts its overall sharpness, but its nothing some PP can fix. Look at Todd Owyoung's ISO 6400 images(ishootshows.com). Very clean and still sharp. I also like the dynamic range in Nikons over Canon. Doesn't matter too much if you shoot RAW though.
Lenses: Hands down to Canon. Options, options options. And cheaper most of the time. Nikon really lacks in primes though. I read somewhere that quoted Nikon saying something along the lines of: only PJ's use primes, and that market is small. Though I don't know how much truth that holds, because I would think a PJ would want the flexibility of a zoom. Plus unless you're shooting with a D300 or better, 2.8 won't be fast enough at times. Canon has a plethora of lenses for that. Nikon may also never have a f1.2 autofocus lens because of how small the f mount is.
Flash:I think Nikon's CLS is far better than what Canon has. However wireless triggers negate that. One can use older and cheaper flashes with pocket wizards or cactus triggers and achieve the same, if not better results(but this extends to Samsung/Pentax and Sony/Minolta).
I'd heavily consider the type of shooting you'll be doing and your budget before buying either system. I think both are good, but I think the "you" part of your photography is gonna be more important than which system you buy into. A lot of my input is from someone who can only afford a consumer body and some decent glass. If you're in my boat, I personally would prioritize learning photoshop, since you probably already know how to use a camera manually well enough. I mean no offense to some people out there, but I've been blown away by people using cheap bodies and or third party lenses, and disappointed with results I've seen from those with much more expensive pro equipment.
If I had to start from scratch with little money and buying used? I'd get which ever is cheaper. The only deal breaker to me really is the fact that Canon has more lens selection, but since I can't even afford most of that(a bag of L's are gonna be worth more than my car!), i'm gonna shoot third party. Everything else i've mentioned is really negligible at my budget.
If I had a lot of money to buy new? I'd get a D700+24-70mm f2.8 and call it a day. ISO6400 @ f2.8 on full frame would probably be what I get on ISO 800 @ f1.4 on crop sensors.
If it helps any, the only shooting I take seriously is concert photography. I love live rock music, and it's a pleasure to shoot it. I love the challenge of capturing fast movement, in low lights, with people to fight with for position and safety. In my case, I just need a fast wide or normal prime(hence my 30mm 1.4), and a body that has decent high ISO. Luckily I can also use that as a walk around and indoor lens. So I can really get by with just one lens. You can see how either system fits the bill for me. Your needs might be different and not as simple. Luckily for me I find most other types of photography boring. Again, I mean no offense to anyone but I'm weird in that I like situations where there are variables outside of my control affecting my outcome(like surfing). However, I do want to get into some strobist fashion photography