Nikon A100 has a
20.0MP 1/2.3' (6.17 x 4.55 mm ) sized CCD sensor . On the other hand, Nikon S3100 has a
14.0MP 1/2.3-inch (6.17 x 4.55 mm ) sized CCD sensor and features Expeed C2 processor.
Nikon A100's sensor provides 6MP more than Nikon S3100'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 A100 and S3100 sensor size comparison.
Nikon A100 and Nikon S3100 have the same sensor sizes so they will provide same level of control over the depth of field when used with same focal length and aperture. On the other hand, since Nikon S3100 has 42% larger pixel area (2.01µm2 vs 1.41µm2) compared to Nikon A100, it has larger pixel area to collect light hence potential to have less noise in low light / High ISO images.