Canon does seem to have improved its noise-reduction algorithms from the S95, although it's also possible the S100 just has a cleaner sensor. Whatever the reason, the S100's ISO 1600 shots look better than the S95's. That said, the S100 also seems to expose a little darker and slightly warmer than the S95.
(1/25 sec, f2.0, ISO 1600, evaluative metering, AWB, 24mm)