My 2 cents.
If your application can tolerate a non-linear voltage drop, two shunts for two ranges (say, 1 mOhm for 100mA-100A and 1 Ohm for 100nA-100mA) in series, with a pair of clamping high current Schottky diodes over 1 Ohm. You may have a problem with the forward leakage of Schottky diodes though * .
With a single 10mOhm shunt capable of 100W dissipation you'll get 1V max drop at 100A and the noise level below 100uA. You would need to watch out for thermal voltages in this version.
A 1mOhm shunt + a sensitive DC current clamp, capable of sensing microamps and at the same time of surviving a 100A overload is another possible option.
Cheers
Alex
P.S. - * it is possible to make an accurate MOSFET "soft" (i.e. no hard switching) clamp at, say, from 100mV to 150mV over 1 Ohm shunt, that would allow for more accurate measurements at the low end of the range.