Nikon D40X vs Nikon D90 - ISO, and sensor uestion?

The Nikon D40X starts at ISO100.
The Nikon D90 starts at ISO200.

Which starting point is better, ISO100 or ISO200?

I'm willing to sell my Nikon D40X and buy a D90. I need the built-in focus motor for the 50mm f/1.8 lens.
I heard the D90 uses a CMOS sensor. Is it as good as a CDD sensor (D40X) in terms of quality?

You will never see the difference between 100 and 200 ISO

Again, CCD or CMOS, not a big deal.

The D90 (or newest D7000) can auto-focus using the Nikkor AF 50 mm f/1.8.

Your fears are unfounded

As time and technology moves forward, sensors get better and better. Since the D90 has a newer sensor, it is better than the D40x sensor

The D40X and the D90 are not in the same league. You will be moving from an entry-level camera to a unit that is best-in-class (yes, better than the new D7000).
The performance of the D90 at 400 ISO is superior to the D40X at 100 ISO: in fact, you would be hard pressed to see the difference at 800.

CMOS sensors are CCD sensors, but they are CCD sensors with separate image processing at each sensor well. The technical difficulties that once made these too difficult to manufacture are long past, and they are the reason that Nikon and Canon have been able to produce such sophisticated, high-speed cameras. In terms of quality, the CMOS sensor in the D90 is very much superior to any CCD you are going to encounter in any camera.