According to the 328 datasheet there is an electrical specification limit of minimum Aref voltage of +1vdc, so getting resolution of .1mv per count just isn't possible without external amplification.
The MEGA (atmega2560) has 4 ADC channels with optional 10x and 200x gain. If you used that one with the internal 1.1v reference you could get pretty close to 0.1mv per count. Of course, reading the datasheet further you can see that the last two bits are garbage (this is a sad fact of life with most ADCs, especially those integrated into uCs), so in the 0-100mv range (with 10x gain on and 1.1v ref) the best you can do is about 1/2mv.
There are however many nice and easy to use ADCs out there. TI may even give you a free sample.