How to regulate a flyback transformer to have output of 100mv or 200mv ripple?
With those modest current requirements (30-400uA), why not just use an LDO on the output as  post regulator?  You don't mention the voltages, so that may not be an option.  If the voltage is higher than 36V, then you'll have to start looking at RC or LC low-pass filters.
For the filters you'll have to know the highest frequency of the ripple and just filter it.