The lenses should be a big factor.

Well, in my experience, Nikon tends to have better glass in their lenses on average, and thus their lenses cost a bit more than Canon. But I wasn't too happy with the Nikon D100 I played with, among other things it seemed a little too complex compared to F100 film camera, and even that was more complex than I wanted. However, as with all things, I'm sure the learning curve is something that can be overcome.

On the other hand, if you go with Canon, as I intend to, with the D10, just stick with good glass lenses, like those in the L series. I've also been impressed with the compatible versions of the high end Sigma line, namely the 180mm 1:1 Macro lens. Here you get a great quality lens without having to buy the Canon name.

[edit]
I think I forgot to mention the main reason why lenses are important. I imagine a digital cameral will get retired after a few years in play, as technology improves. You will probably update the camera, but you'll end up keeping the lenses. I started out with a Rebel 2000 a few years ago, bought canon lenses, then I moved up to the EOS3 (love it!!!), upgraded some lenses, kept others, now I'm looking to get a D10 to add to the bag. I use an S50 to hold me over till then (love it!!!)

Greg