as hillbilly states above - feel the camera in a shop. Hold it, look through the viewfinder, have a quick look at the menu system etc. The Nikon lens range is pretty darn big as well, there are very few lenses that a beginner/enthusiast will want/need/able to afford that the Nikon range lacks.
The 18-55mm that comes with the 1000D is I believe the non-IS version - which by all accounts is a bit of a dog, canon's 18-55mm lens with IS which comes with all other canon dslrs is far better.
The Nikon 18-55mm VR lens that comes with the D3000 is supposed to be one of the best kit lenses available. The Nikon also has a bigger rear lcd. Plus it has spot metering which the canon lacks, however the canon has liveview which is useful for macro photography.
There isn't much to choose between them, but if they are the same price and after handling them you still aren't sure I'd choose the Nikon, because it comes with a better kit lens. One thing to remember with the D3000 it will only autofocus with nikon lenses that has an af-s motor - the only lens this really affects is the 50mm f/1.8 - if you want a 50mm prime with AF you'd have to buy the f/1.4. however on the other hand Nikon have the cheap af-s 35mm f1.8 which is imo a more usable range.
just my view on it (I'm a sony user by the way so I'm unbiased on this one!)