For starting up you could wire the pc power up thru a relay which would energise when you turn your cars ignition to accessory. The problem is the next progression is starting the car, with the starter motor sucking alot of juice, often causing a PC to faulter - not always, but is normaly the case.
The other method is just to have a switch, you can make it look elegant if you like I like having a seperate switch independent of the car - it also saves hacking into the cars electricial system.
For powerdown just cutting the power is easiest. If you are going to use a ATX motherboard you could shutdown properley using a shutdown controller (search the BB), but I much rather have instant turn-off and just disable scandisk. Of course if you run DOS you dont even need to worry about that.
Its not bad for a HDD to just cut power, it can cause lost clusters if the hard disc was writing data back to the hard drive at time of powerdown..... but with playing mp3's etc.. this would not normally be a problem.