I shot the Nikon D3100 with my Nikon 50mm f1.4G, and my Nikon D90 with my Nikon 50mm f1.8D. Shot them both at f2.8, as both lenses are tack sharp and virtually identical for sharpness by f2.8.
Lighting is fairly low, from overhead compact flourescent bulbs. I've left the images with the color as shot out of camera. No color correcting for white balance has been done.
The conclusion from these samples and all the shooting I've been doing in the last couple weeks... the Nikon D3100 is about a stop better at high ISO. Maybe not quite a full stop, but bear in mind the D3100 has an extra 2 megapixels on the D90, so close to a stop better is VERY impressive.
Also, at the higher ISO settings I find myself liking the image color better out of the D3100. The color from the Nikon D3100 at higher ISO settings seems to hold together a little better than the D90 colors.
Here's some side by side composite images I put together from D3100 and D90 images at ISO 800, 1600, 3200, and 6400. The full size images are over at my Nikon D3100 vs Nikon D90 Flickr page.
The images are all processed in Nikon's ViewNX2 as Lightroom 3 doesn't support the D3100 at this time. Images are all as shot, no editing done, and saved at the High Quality JPG setting. They were cropped at full resolution, and as you can see, no re-sizing has been done, so the D3100 images are a little bigger than the D90 images.

Nikon D3100 vs Nikon D90 @ ISO 800

Nikon D3100 vs Nikon D90 @ ISO 1600

Nikon D3100 vs Nikon D90 @ ISO 3200

Nikon D3100 vs Nikon D90 @ ISO 6400
Here's the full stack of ISO 800 through 6400 from the D3100. Feel free to download it from the Flickr page and compare it as you will against the D90 stack below.

Here's the full stack of ISO 800 through 6400 from the D90.

These images are cropped from the full size image. The full size images on the Nikon D3100 vs Nikon D90 Flickr page have more in the photo to compare if you want to do further pixel peeping.
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