Nikon S9100 has a 12.0MP 1/2.3-inch (6.17 x 4.55 mm ) sized BSI-CMOS sensor and features Expeed C2 processor. On the other hand, Canon 6D has a 20.0MP Full frame (36 x 24 mm ) sized CMOS sensor and features Digic 5+ processor.
Canon 6D's sensor provides 8MP more than Nikon S9100'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 S9100 and 6D sensor size comparison.
Sensor Size and Resolution Comparison image of Nikon S9100 and Canon 6D Cameras
As seen above, Canon 6D has a 30.8x Larger sensor area than Nikon S9100. 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.