A CCD exposes the entire image all at once, while a CMOS sensor (at least, all those on the market today) exposes one horizontal scan line at a time, top to bottom. This is called a rolling shutter. The result is that your target, if it's moving (or you're moving, taking video) can be skewed or wobble, because it was in one place when the sensor recorded the top of the image but is in a different place by the time the sensor records the bottom of the image. You can even end up with wacky exposure issues if you're at an event and someone else's camera fires a flash while you're taking a photo or recording video you can end up with part of your frame light and part of it dark.
That said, a CMOS sensor is more energy efficient, and does not have the issues a CCD has with bright lights causing overloading resulting in a vertical smear in the final image.
So my feeling is that if you're going to shoot video, or a lot of stills of moving objects, go CCD. If the issues noted with CMOS sensors are not a problem for you, I have no other reasons to avoid a CMOS sensor.