"На машине большие окна" - would mean that several big windows (plates of glass and frames) are actually lying separately on the car - either on its roof, hood etc.
"В машине большие окна" - would mean that several big windows (plates of glass and frames) are actually put inside the car (on the seats, for example). But people would understand you if you meant the built-in windows.
"В машине окна запотели" is said when built-in windows are foggy from the inside of the car.
But you can't travel "on" a car (unless you're clasping onto the roof), and car components, even ones unambiguously inside the car body can still be referenced with "on." "There's a good engine on that car."
I'm sure road-legal aircraft will bring their own inter-language complications ;)
TimK is right on all counts, but as a peculiarity, if you are talking about windows of a house, you can say both "у моего дома три окна" and "в моем доме три окна". And even "у меня в доме три окна".
У and в in the case of a house mean a slightly different thing though. At least when saying у дома, I sort of imagine looking at the house from the outside. And when saying в доме три окна, I kind of imagine looking at the windows from the inside. Not sure if this explanation makes any sense, sorry...
It's actually fairly simple, I think. When we use "у" + genitive, we talk about a feature or a characteristic of the object. Here, the windows (as doors, engine, brakes, seats) is an integral, inseparable part of the car as a whole. When you want to describe something that is actually inside the body of the car (doors and windows are not), you use "в" + prepositional/locative. Since you can think of the engine (or seats, airbags, etc) this way, you can also use "в" but this often leads to stylistically unnatural sounding.
I guess the takeaway is Russian treats cars' having of things more like people's having of things and less like buildings' or rooms' "having" of things. Or perhaps I err in the thought elicited somewhere or other in the tree that "В комнате деревянный пол" would be a more common turn of phrase than "У комнаты деревянный пол" for expressing the idea of "The room has a wood floor" (whereas situations where I would say "There is a wood floor in the room" don't immediately come to mind).
Well, we probably realize the floor (and the ceiling) not as a feature of a room but as something lying on the bottom face of the room's prism. Parquet, for instance. Or tiles. This is why we only use "в".
This theory still doesn't explain why "В этом доме высокие потолки", though.