i would classify myself as a amateur dslr photographer. when i had to choose between the Canon XT and the Nikon D40 in the summer of 2007,i ended up choosing the nikon because it felt a little better in my hands. the controls were easy to get used to, and i knew what i wanted out of the camera.
since then, i have upgraded several lenses (the kit lenses usually are not the best) and am about ready to step up to a bigger and better body, but will stick with nikon because of the lense/filter/memory/etc choices i made.
you should hold both and decide which is right for you.
i believe both are pretty similar in terms of price, build quality, image quality, etc when you stay below ~$2000. when you go north of that, i would go one way, CANON, mostly because of the choice of lenses (think L lenses).
skip the d3000. the d5000 is a much better camera, but the lens isn't the best. i updgraded the kit 18-55 to the 18-105 VR and the image quality is a night and day difference. the same can be said with my 35mm and 50mm f/1.8 compared to the kit 18-55.