It depends on tech level of the car and how difficult for you want the system to be and WHY YOU WANT TO PREVENT THE CAR FROM STARTING. The why part is very important because if you just want the car to not start, the ignition key/switch is the most obvious way and has been in use for a really long time. If you want to prevent someone form stealing your car, you'd need to know what would the thief be capable of and how difficult you want the system to be for day to day use. I mean, you could always take the battery with you, but that would add a few minutes of setup time every time you want to start the car, plus problems related with carrying the battery.
Some cars have electrical central locks which will not work if the battery is disconnected. It could also cause problems with internal clocks, microcontroller settings, radio settings and so on.
If you want to stop the car from starting, maybe it wouldn't be a bad idea to put some sort of switch at the starter itself. This way, the rest of the car's electronics could still work. To me this looks like the safest place because, as far as I can see, attempting to start a car with disconnected starter will cause the least amount of damage. Please note that the last car I worked on was a Volkswagen Golf Mk1 and that was quite a while ago, so I'm probably out of date.
Another idea would be to analyze how car's starting procedure goes. Some cars have a key controlled rotary switch which is used to start the starter. If you add another switch in series with the starter switch, you could prevent car from starting.
Some other cars I've seen have a start button which is directly connected to a microcontroller, and they would be a bit more difficult to intercept.