I must admit a little confusion over the topic of resolution. Or rather, confusion over why other people seem to be confused about resolution.
It is my understanding that the Fuji S2 is basically a 6 MP camera. The 12 MP max resolution advertised is done by some in-camera software interpolation.
While FujiFilm probably makes claims to the superior method they may use to do that interpolation it is still interpolation.
You can do similar interpolation in Adobe PhotoShop. In addition, if you own a program like Genuine Fractals you can "up-rez" your photos. But, basically, you can't create "true" resolution from nothing.
If someone has more qualified information on this I'd love to hear it. Otherwise, I believe the S2 and the D100 are both 6 MP cameras and, therefore, of equal capability with regard to resolution.