Canon SX1 IS has a 10.0MP 1/2.3" (6.17 x 4.55 mm ) sized CMOS sensor . On the other hand, Fujifilm S1 has a 16.0MP 1/2.3" (6.17 x 4.55 mm ) sized CMOS sensor .
Fujifilm S1's sensor provides 6MP more than Canon SX1 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 SX1 IS and S1 sensor size comparison.
Canon SX1 IS and Fujifilm S1 have 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 SX1 IS has 59% larger pixel area compared to Fujifilm S1, it has potential to collect more light on pixel level hence have less noise in low light / High ISO images.