The only place I see that sort of thing making sense is if it's running through mountains, but I definitely agree that if it does we should do something like Sy has. Also maybe if it goes under an ocean we could have it run underwater for a bit too, but if it is going under some plains or a desert there's no point to popping up and it'll just ruin the landscape.
Also while I was messing around in creative yesterday, I came up with an idea that could replace rails altogether, based upon jumping between boats that are a set distance apart from each other. Basically make two parallel lines of glass and then plop a boat down every four blocks, so there are three blocks between each. If you can right click 5 times a second, you are going almost 3 times the speed of a max speed minecart. Also it doesn't require shittons of iron or gold. It is a lot easier to screw up than minecarts however, but most of the time if you do break it you would have done it on purpose (e.g., getting out of one of the boats halfway through and pushing it somewhere, or placing a water bucket down)
The same concept also works brilliantly as an elevator, most importantly with a stop on each floor. Then you just have a water break along the back and you have the most versatile elevator I've ever seen, without one piston or any redstone. What do you guys think?