Fujifilm S9800 has a 16.0MP 1/2.3" (6.17 x 4.55 mm ) sized CMOS sensor . On the other hand, Canon SD1200 IS has a 10.0MP 1/2.3-inch (6.17 x 4.55 mm ) sized CCD sensor .
Fujifilm S9800's sensor provides 6MP more than Canon SD1200 IS's sensor, which gives a significant advantage in real life. You can print your images larger or crop more freely.
On the other hand, please keep in mind that Max sensor resolution is not the only determinant of resolving power. Factors such as the optical elements, low pass filter, pixel size and sensor technology also affects the final resolution of the captured image.
Below you can see the S9800 and SD1200 IS sensor size comparison.
Fujifilm S9800 and Canon SD1200 IS have the same sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Canon SD1200 IS has 59% larger pixel area (2.81µm2 vs 1.76µm2) compared to Fujifilm S9800, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.