Sigma SD9 has a
3.0MP APS-C (20.7 x 13.8 mm ) sized CMOS (Foveon X3) sensor . On the other hand, Sigma SD1 has a
15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual True II processor.
Sigma SD1's sensor provides 12MP more than Sigma SD9'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.
Another similarity between these two cameras is that both Sigma SD1 and Sigma SD9 sensors lack anti-alias (Low-Pass) filters. Removing anti-alias filter increases the sharpness and level of detail but at the same time, it increases the chance of moiré occurring in certain scenes.
Below you can see the SD9 and SD1 sensor size comparison.
As seen above, Sigma SD1 has a 1.3x Larger sensor area than Sigma SD9. Larger sensors give photographer more control on the depth of field and blurry background compared to smaller sensor when shot in same focal length and aperture.