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I have a high-end Nikon, so perhaps I'm not the best person to give you advice on the lower end DSLRs, but both Canon and Nikon have a large variety of lenses and other accessories. Both of them make good choices as camera systems if you consider moving up to more lenses or different bodies later. And with Nikon and Canon, you certainly have the option of renting special purpose lenses that you would not want to own due to expense (you can rent from places like Calumet).
If you plan on just picking a camera with a packaged lens and don't plan on adding more latter, then other brands might serve your needs just as well.
Joe made the comment that the D50 is better for macro, but that is mostly a function of the lens, not the camera body. Of course, the entry level DSLRs probably often come packaged with a lens anyway, so perhaps the lens packaged with the D3000 is not as good for macro? You can always buy different lenses.
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