Whenever you digitize something, there is going to be some amount of information lost. When the original is reconstructed, that loss of information may lead to results that have little to do with the original signal. That applies to sound, electronic signals and to light patterns projected onto an imaging sensor.

As long as the things we digitize are larger (have a lower frequency) than the resulting digital signal, then the original can be reconstructed with at least decent fidelity. (The maximum frequency that can be faithfully digitized must be less than half of the sampling frequency. It might help to look at the Wikipedia entry for Nyquist frequency.)

When we try to take digital samples of objects with fine patterns, like regularly-spaced lines, the sensor might not be able to keep up, and when the picture is reconstructed we wind up with a moiré pattern, which generally shows up as an area of false colours in a digital image. Instead of the fine pattern, you'll get a splotch of colour that isn't in the original, or lines running at opposite angles to the lines in the original pattern.

To get around the moiré problem, most small-format (full-frame 35mm and smaller) digital cameras incorporate an optical low-pass filter into the sensor assembly. Essentially, its a filter that blurs the image somewhat so that there are no harsh transitions at a finer level of detail than the camera can accurately reconstruct from the sensor recording. The "ordinary" D800 works in exactly that way.

With the sensor resolution now sitting at over 36MP, though, there are a lot fewer instances where the detail you are trying to record cannot be resolved and reconstructed accurately -- especially if you are working in a studio situation and can change things if you bump into the Nyquist limit and create moiré (changing the magnification to make the pattern larger so that it can be resolved properly, smaller so that it doesn't really resolve optically due to limits of the lens, or changing depth of field are all ways of attacking the problem). In order to get the maximum image resolution, then, it might be worthwhile foregoing the low-pass filter, as medium-format DSLRs (and a few high-end cameras, like the Leica M9) do.

Now, you might think that taking something out of the camera should cost less than putting it in, and you'd be right. The D800E doesn't exactly leave out the low-pass filter; it has a sandwich of filters instead. There is still a thin low-pass filter, but it's backed up by another thin filter that largely undoes the effect. That allows the cameras to be produced with the same basic tooling and tolerances. Leaving the low-pass filter out of the equation would make the sensor thinner, and require different mounting and alignment to keep the focal plane in the same position relative to the lens mount flange and the reflex mirror. The extra $200-300 for the modified sensor is probably a lot cheaper than a whole different tooling setup for the body castings.

The upshot is that the D800E should be able to take sharper and more detailed images, but it does that at the risk of creating moiré patterns in areas of fine detail. Both cameras may have the same number of pixels, but the D800's pixels will be "mushy" when compared to those from the D800E.