Isolation and Amplification Circuit for reading multiple analog voltages
One way to do this is to make a small isolated supply, like maybe a flyback converter.  Transformers aimed at POE (power over ethernet) are usually well suited for such small isolated supplies.

Once you have a isolated supply, you can run a small microcontroller with A/D and serial port.  There can be analog circuitry in front of the A/D to amplify or condition the signal as necessary.  The micro converts the signal to digital, which it then sends out serial over a opto-isolator.  The main micro then reads these values over its UART intead of it A/D.