For your specific question, in the past I've used one analog input like my first diagram and done the level detection/ladder in software. It can easily be modified then.
For your on/off switch input (my diagram 4) you can substitute a 4049 for an inverted signal - it may depend if the state matters when everything is first powered up.
Below is what I've distilled from articles such as the ones linked, and some experience with dead electronics in cars.
Parts I've used are because they are local or I already had them, so you might find better parts.
Some might be overkill and you could substitute for sanity.
Any input should have schottky diodes and a resistor at minimum. I've avoided ordinary zener diodes as they can affect the input, and the schottkies probably do a better job anyway.
I use low-ish value voltage divider resistors to ensure a reliable analog read.
Analog input, suitable for automotive voltages
Another analog resistive sensor input, and a Dallas Onewire input:
Switch input, debounced, switch to ground, not linked to vehicle voltages
Another digital input from vehicle switches that are on or off with full vehicle voltage swing, like headlight switches for example
The +5v supply, Vcc in my diagrams, for pullups, schottky diodes and anything except the Arduino itself should have a separate supply. This ensures any pulses, noise or otherwise returned via the protection diodes is handled by a separate regulator and NOT the Arduino internals.
The LM2940 is specifically made for automotive use, but you could substitute the ordinary old 7805. The tantalum caps pictured near the regulator should be physically very close to the regulator.
I have the Arduino itself powered by a semi-filtered supply - if the onboard regulator gets hot stick a couple of 1N5401's or 4.7R 5W resistor in series just to drop the supply voltage a bit. In the past I've used one of those cheap adjustable Arduino switching supplies set to 10v. They work great.
Powering the Arduino via it's barrel jack or the Vin pin gives the most protection. I wouldnt try to power an Arduino Mega2560 via 5 volts in an automotive environment unless it is extremely close to the regulator - best to let some filtering and the onboard regulator do their job.
You can run 3 or more Arduinos from this baby:
Overall, I've gone fairly complicated, so use what suits you and your reliability requirements.