LOL Gentoo, let me say it another way.... when I look at my photos shot at base ISO at 100%, they are all about as sharp as each-other. Doesn't matter what camera I shoot them on. What makes the D90 such a better camera for me is that it gives me a higher % of keepers. It does things like correcting chromatic aberration. Active D lighting, It's clean enough to shoot at higher ISO's, which means I have less motion blur. The AF system is far, far more accurate. I can use picture controls to get the colors I want.
All of these factors let me get more keepers per shoot. But when I compare a good shot that I took with my D40, to a good shot I took with my D90, I can't tell you which is which. Viewed on my computer monitor, both cameras are thowing away most of their pixels. I want a CMOS D40, because I love the size, but miss the features of my D90. I don't care about the pixels.
Print is a little different. Photo printers can print north of 300 DPI. A photo that fills up my 24 inch (1920 X 1200) iMac screen would print out as a 6.4 X 4.0 inches at 300 DPI. Some printers can go well north of 300 (good luck being able to tell the difference, but the dots are in there). For Print, MP's matter. At 300 DPI, the D90 would print at 100% as a 14.2 X 9.5 inch... about as big as I'd ever print something. If I had a D3X, than my 5690 X 3964 image would print 19 X 12.3 inch print at 100%. That's about twice as large as my D40's 10 X 6 prints. But I needed 4x the pixels.
If I need to print any larger than 19 X 12, then I'm going to have to get back a little ways in order to look at the whole image. The further away I stand, the harder it is for my eye to detect differences at the pixel level. 6 feet away, I'd be hard pressed to tell any difference in sharpness between a 24 inch image printed at 300dpi and the same image on my monitor at 70dpi (I didn't do the math on the monitor, but I think most of them are right around 70 these days).