Samsung NX100 has a 15.0MP APS-C (23.4 x 15.6 mm ) sized CMOS sensor and features DRIMe Engine processor. On the other hand, Fujifilm X-M1 has a 16.0MP APS-C (23.6 x 15.6 mm ) sized CMOS X-TRANS I sensor and features EXR Processor II processor.
One other difference between these two cameras that is worth mentioning is that Fujifilm X-M1'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 moire occurring in certain scenes.
Below you can see the NX100 and X-M1 sensor size comparison.
Samsung NX100 and Fujifilm X-M1 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.