Why is the Nikon D90 more expensive than a Nikon D3100 (Body only)?

If you turn a blind eye to the cheap feel of the Nikon D3100 over the solid feel of the Nikon D90, On paper the Nikon D3100 has higher "Spec" over the elderly Nikon D90.
The motorised body is not an issue as my lenses all have the built in motor into the body.
For example the Nikon D3100 has better low light performance with higher ISO settings. The images at ISO 3200 on the Nikon D3100 are still very impressive and even ISO 6400 is still OK. On the Nikon D90 there's a lot of "digital noise" in the image at ISO 3200. And at ISO 6400 the Nikon D90 looks like the image was taken on a £50 ($80) mobile phone.

Because it's a more serious camera. The D90 may have metal parts where the D3100 has plastic. The D90 also has better seals.

There's a lot more to a camera than the pixel count.

The D90 has upgraded features, such as:

-In camera motor for focusing AF lenses.
-In camera remote commander for controlling speedlights wirelessly.
-High-speed FP sync for 1/4000 flash shutter speeds.
-Wired and wireless remote capability.
-Nikon brand accessories; battery grip, etc.
-top LCD for direct display of camera settings (don't need to use the rear LCD to check settings).
-higher end build.
-higher capacity battery.

While the D3200 is indeed a nice camera, and the D90 is a few years old, they are targeted for different users. The D3200 is an entry level camera, for users just getting into DSLRs. The D90 is targeted for advanced users that need the features that I have listed above.

And I do realize the D90 has a limitation in the ISO, and I rarely go higher than ISO 800 on mine.

But don't discount the lens. With my AF 80-200mm lens on my D90, it is a f/2.8 at 200mm, which is much superior to the AF-S 55-200mm lens, which is f/5.6 at 200mm. This is a two stop improvement, so if you needed to use ISO 6400, the D90 could use 1600, as the lens improves the light gathering capability. So in reality, your lenses are more important than your camera body.

Unfortunately, the D3200 can't autofocus the AF 80-200mm f/2.8 lens. If you want an equivalent lens, you need to buy the AF-S 70-200mm f/2.8 lens. The price difference? The 80-200mm lens is $1, 200 and the 70-200mm lens is $2, 400.

So unless you need the AF-S (slightly faster focus speed), or the VR of the 70-200 - if you buy the 80-200, you will save enough money you could also buy the D7100 as well.

If you compare the Nikon D3100 to the Nikon D7000, you will be comparing cameras of a similar technology.

The D90 was introduced the same time the D60 was.

In 2008, low light performance of sensors are not nearly as advances as they are now, so it is not a surprising that you will get noise under those conditions on a camera that is that old.

I really doubt that a cell phone image at 100% out does the D90.

There's also something to be said about the skill level of the user

Here is a shot taken at 3200 ISO using an older D300 (circa 2007)

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As you can see, there's little noise in this shot.

If you do not need the robustness of the D90/D7000/D7100, you may want to look at the Nikon D3200.It performs very well under low light conditions.

A link you can exploit to see how various sensors perform in low light

http://www.dxomark.com/...nd3)/Nikon

As you can see, the D90 does slightly out perform the D3100 in low light conditions. What this tells us is that to get the most out of ANY camera, there are some special skills that go beyond just the specifications and lab tests

"The motorised body is not an issue as my lenses all have the built in motor into the body. "
It may not be an issue or you, but for others and for the price of the camera.