Most cars with manual transmissions shut off the injectors when your foot is off the gas, and the car is in gear. Most of these vehicles however, require a certain engine speed to shut off the fuel. For example, my nissan requires the engine to be spinning at more than 2400rpm. My brothers dodge requires around 1800rpm. Below those points, the engine is burning more gas than it would if you simple took it out of gear. You could say “put the car in a lower gear to increase engine RPM” but then you’ll have a much stronger engine braking effect, which may not be desirable.

Also, this generally doesn’t apply to vehicles with automatic transmissions. You can save large amounts of gas by shifting to neutral in certain circumstances, but this often raises safety concerns, as well as concerns on transmission wear and tear. Likewise, shifting to neutral at stop lights will save marginal amounts of gas (in my van’s case about 35%, but keep in mind that since the amount of fuel required to idle is small, any fraction of fuel saved will be small)

Also important to note, by taking the car out of gear, you can pick up speed downhill, and coast for much longer distances. In many situations, this more than offsets the small amount of gas required to idle.

Are you referring to short shifting? By shifting early in a manual car, you can bog down the engine by shifting early into a higher gear. This is not particularly good for you engine, and you’re right its less efficient in terms of “Gas In vs Power Out”. However, until you’re at an excessively low RPM, your vehicle uses so much less gas in the next gear up, that the efficiency difference, especially in modern day engines, is trivial.

Keep in mind, you’re engine is most efficient at its peak torque, this speed carries from engine to engine, but I guarantee that if your engine operated at that RPM regularly, you’re burning several times as much gas as you need to.

Also, in regard to windows up/down on the highway: It completely depends on the car. Some vehicles will have their aerodynamics ruined by having their windows down, some will not. Likewise, some vehicles are very aerodynamics to start with, and a little more from the windows wont be noticeable. Likewise, setting the AC to 60 in 100 degree heat uses much more fuel than setting it to 70 in 80 degree heat. It all depends.