Sony NEX-3 has a 14.0MP APS-C (23.4 x 15.6 mm ) sized CMOS sensor and features Bionz processor. On the other hand, Sigma Quattro has a 29.0MP APS-C (23.5 x 15.6 mm ) sized CMOS (Foveon X3) sensor and features Dual TRUE III processor. Sigma Quattro's sensor provides 15MP more than Sony NEX-3'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 NEX-3 and Quattro sensor size comparison.
Sony NEX-3 and Sigma Quattro 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.