Fujifilm X100 has a 12.0MP APS-C (23.6 x 15.8 mm ) sized CMOS sensor and features EXR processor. On the other hand, Sigma DP3 Merrill has a 15.0MP APS-C (24 x 16 mm ) sized CMOS (Foveon X3) sensor and features Dual TRUE II engine processor.
Another difference between these two cameras is that Fujifilm X100's sensor lacks 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 moire occurring in certain scenes.
Below you can see the X100 and DP3 Merrill sensor size comparison.
Fujifilm X100 and Sigma DP3 Merrill have almost the same sensor size so none of them has any significant advantage over other in providing control over depth of field when used with same focal length and aperture.