I have used both and can find fault with both along with many strong points too.
All of the below are my own opinions so please don't slag me off if you don't (and most probably won't) agree.
For me Nikon has better cheap glass, the lens and body build seems better (up to D200/300 level) and I think macro images are often a little sharper. But the main difference IMO is that Nikon seems to take other glass better than Canon (sigma and tamron lenses). Nikon Cameras are a little easier to use IMO.
Canon I feel is better with tele lenses and has a slight edge in detail here. The settings seem much more sensitive and for an inexperienced user you are more likely to either under or overexpose an image, I find with canon you have to be bang on and with Nikon you have a little more room for error (probably due to images underexposing slightly by default with Nikon). Nikon I feel has slightly truer colours straight from the camera though.
Canons high end glass is a bit cheaper and I feel the IS works better than the Nikon's VR (this may have changed since it was a year or two since I tried Nikons).
Noise - Nikon gets slated here but I found both cameras to be quite similar I have to admit.
So what do I use? Canon but Im going back to Nikon for my macro work, I just enjoyed using it more and IMO it had a little edge, as simple as that.
At the end of the day cameras perform as well as the user, but if one needs to be picky then thats what I found.
Like I said these are my opinions, I don't recommend one over the other, both are great, but the grass is often greener.
Kris