To simplify things a great measure... The CCD or (cmos..who would use that?!) is that which replaces film, it's what captures the image. All else being equal the larger the film area the better right. With CCD's even of the same pixel count this is true. The larger the CCD - the less noise (as a general statement).
Yet I regress, back to the simplistics. Even if the CCD's were of the same quality does that make the camera equal?!? If so we should all stop wasting our money on Nikon SLR's and buy Fuji Discovery's! (no I'm not knocking Discovery P&S - they are great P&S's) They both will use the same 35mm film.
I always laugh at the digital marketers, all they really push is the pixels - don't get me wrong that's important and why the D100 has me drooling - but what ever happened to traditionally important things like GLASS ? Heh, heh the D100's got that too!