Hi. I'm going to make 9 fuel cells running individually(Each one produces less than 5V) and I would want to log the potential difference between each pair of electrodes in every single cell. I read than an arduino can't handle many inputs or measure differential voltages by itself. Maybe someone could help me on what hardware is required? Thanks.
Put a multiplexer on the analogue input to get more inputs.
You can not connect the fuel cells directly unless it is floating with respect to the Arduino, in which case you can use relays to switch one cell only into the Arduino.
Otherwise you will have to use the "flying capacitor" technique.