Use a toggle switch mounted in the front of your car (momentary on) connected to your power switch on the PC. Then run a line from the 12 volt power connector inside your PC, and connect this to a relay to toggle the constant power supply (directly from battery, use an inline fuse). Then connect your accessory power lead after the relay. This will allow power to the computer for startup (when key is in accessory position or run position). But after you turn off the car, press your toggle button in the front of the car which will allow the computer to shutdown. After the computer shutsdown, it will open the 12v circuit on the constant power line. Killing all power to your computer (also usefull if you use an inverter)
Thus giving you a cheap shutdown controller.... BTW this was discussed in the forums once before. But this is a good refresher.