Nikon S6100 has a
16.0MP 1/2.3-inch (6.17 x 4.55 mm ) sized CCD sensor and features Expeed C2 processor. On the other hand, Sigma SD1 Merrill has a
15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual True II processor.
One other difference between these two cameras that is worth mentioning is that Sigma SD1 Merrill's sensor doesn't have an anti-alias (Low-Pass) filter. 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 S6100 and SD1 Merrill sensor size comparison.
As seen above, Sigma SD1 Merrill has a 13.7x Larger sensor area than Nikon S6100. 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.