They are both good entry level cameras. The D3100 is newer, more compact, and has better noise control at high ISO's. The D5000 has come down in price because it is now being replaced by the D5100. I have a D90 and a D3100 and the D3100 has as good or better image quality.
My first choice would be the D3100 18-55 VR kit and a Nikon 55-300 VR if you can afford it. The extra reach of the 55-300 VR makes a difference. I just replaced my 70-300 VR with the 55-300 VR because it's much smaller and lighter and its image quality is as good or better.
If you can't afford the 55-300 VR, the D5000, 18-55 VR, and 55-200 VR is a very good kit at a very good price.
And, here in the US, the 55-300VR just dropped another $50 (now $250) when purchased with the D3100 kit!
I just sold a D7000 yesterday and had to order the 55-300VR as we had no more in stock and the computer automatically dropped the price of the lens to $250 instead of the $300 it had done just the day before with a different order.
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