Managing spark advance/retard, injector "on" duration, idle speed, etc, based on lots of sensor readings (knock sensors, o2 sensors, mass air flow readings, throttle position, rpm, engine temp, boost pressure, etc).

If you, for example, improve airflow in your car drastically, or install larger injectors, or a high flow exhaust...the stock ECU code/maps may not be flexible enough to optimize for that. Also for bolting fuel injection onto an engine that was previously had a carburetor.