Interfacing with OBD (on board diagnostics) and/or an ECU for programming your fuel injection.
Control windows, air suspension, HVAC and other systems from the PC.
Play movies as digital files instead of DVD discs for mobile entertainment, thus preserving your original discs.
Internet through a Wifi connection or cellphone carrier to have internet access wherever there is a signal.
Cool visualizations for your music that no headunit could come close to.
Play games in your car (really more for passenger entertainment) wihtout being limited to a specific console.
Basically, anything you can do with a PC at your desk, you could do on a PC in your ride. The possibilities really are endless.